Ever since The Los Angeles Times reported last weekend that Attorney General Eric Holder is inching closer to investigating detainee torture that occurred during the “war on terror”, the debate over whether the Holder probe is a good thing has intensified — and distracted a few of us from the spectacle of the town hall brawls.

Andrew Sullivan at The Atlantic called it “the worst of both worlds” because Holder is reportedly considering prosecuting the actual interrogators who exceeded the interrogation limits set out by John Yoo & Co. in Justice Department memos, rather than the authors of the memos and the torture policy themselves.  That “risks essentially legitimizing the torture it does not prosecute,” Sullivan argues.

And on Monday, Digby wrote that the purported impending investigation uses “inverted pretzel logic” to go after only “those who failed to follow John Yoo’s directives.”

Digby continues:  “I think we can all see the problem here, can’t we? By prosecuting waterboarding “abuses” we are essentially declaring waterboarding under John Yoo’s only slightly less sadistic guidelines to be legal. Evidently, the new standard will be that if you’re going to torture, you’d better do it right.”

Well, sort of.  These arguments urge the attorney general to do the right thing, but they don’t take politics into account.  And the attorney general is, above all, a political animal.

Holder knows that his boss, President Obama, and his boss’s chief of staff Rahm Emanuel don’t want prosecutions of the last White House to distract from the Obama agenda. So a criminal investigation of John Yoo, David Addington or Dick Cheney was just not on the table.

But I don’t think there’s any real way for an independent prosecutor to ethically investigate the torture and sadistic abuses inflicted on detainees at Abu Ghraib, Bagram and elsewhere without that ultimately leading up the chain of command – to who ordered what to happen and how. And that’s inevitably going to raise the much broader question of whether the legal memos actually represented a policy that was communicated to interrogators when they were beating prisoners and leaving them in the cold to die (more on that in a bit) or whether the “policy” was just created after the fact to make the whole interrogation process in the early lawless days of the “war on terror” look legitimate.

I realize this doesn’t address whether what those memos themselves describe was illegal, and why that bothers people who think that tactics like waterboarding and systematic sleep deprivation and confining people in tiny boxes with insects ought to be condemned and punished.  But it’s a beginning of finally starting to hold someone accountable. And I’m convinced that if it’s done seriously by a truly independent prosecutor, it will be a key step toward exposing the whole truth about what really happened during those dark Bush years. And, one way or another, the truth will come out. (Don’t forget there’s still that Justice Department ethics report on the development of the torture memos that’s supposed to be issued any day now.)

Holder is likely to investigate some of the cases that were discussed in the highly anticipated still-classified 2004 CIA inspector general report, which is supposedly what got Holder upset enough to consider taking action. (The fact that the declassified report is set to be released on Aug. 24, and is likely to include some really gruesome details, probably helps motivate Holder, who as the nation’s top law enforcement officer surely doesn’t want to look like he’s deliberately ignoring heinous crimes.)

News reports and a series of letters between the Justice Department and Senate Judiciary Committee member Dick Durbin (D-Ill.) that I’ve written about highlight some of the cases likely to get special attention. They include the death of an Afghan man who was stripped naked, dragged across a concrete floor and chained there by CIA operatives in a secret prison north of Kabul known as the “Salt Pit”; he was left on the floor overnight and froze to death.

Then there’s the death of Manadel al-Jamadi, an Iraqi insurgent who died just hours after he was captured and beaten by Navy SEALs, who hung him from his wrists, which were tied behind his back, until he was dead.

And there’s the killing of Iraqi Maj. Gen. Abed Hamed Mowhoush, a 56-year-old who, reportedly uncooperative with interrogators, was stuffed into a sleeping bag and clubbed to death.

Whether it’s a good idea to focus on these sorts of cases, which clearly went beyond the bounds laid out by the Bush Justice Department’s legal memos, or whether Holder ought to be prosecuting the authors of the memos themselves is beside the point. Because the CIA agent who clubbed a man to death or hung him from his wrists on the ceiling or left someone in sub-zero temperatures chained to the floor naked is going to have to explain how he came to think that was acceptable interrogation conduct. And that’s likely to reveal that the bounds we’ve all seen in John Yoo’s torture memos – many of which were drafted years after these murders occurred — were never articulated to the interrogators on the front lines.

In fact, as The Los Angeles Times report notes (and as Digby pointed out), it’s not clear that CIA interrogators were ever even told about any legal memos.

“A number of people could say honestly, correctly, ‘I didn’t know what was in [the memos]’ “ a former senior U.S. intelligence official familiar with the operation of the interrogation program told the L.A. Times.

The Times’ reporters present that as if it’s a defense to the crime that will likely foil Holder’s prosecutions. Actually, it’s strong evidence that it’s the commanders and policymakers, rather than the front-line interrogators, who are most responsible. After all, particularly if they didn’t tell their subordinates what the rules were, then they have what lawyers call “command responsibility” for their subordinates’ actions.  Think of it as the opposite of the Nuremberg defense – “just following orders” – that Bush staffers joked about in the e-mails released yesterday about the U.S. Attorney firings. They just “followed orders.” This is accountability for giving orders.

And isn’t it the higher-ups who knew this stuff was illegal and ordered people to do it anyway that we most want to hold responsible?

I made this point yesterday on Warren Olney’s radio show, “To the Point,” produced by KCRW and Public Radio International. Greg Miller, one of the L.A. Times reporters who wrote the story, was making the case on the air that Holder is going to have a really hard time prosecuting the CIA interrogators. Miller cited the claims of former Justice Department employees who investigated these cases during the Bush administration and did NOT refer them for prosecution because the facts to support a prosecution “just weren’t there.”

At no point during the show, though — nor in his L.A. Times piece — did Miller acknowledge that those former Justice Department officials had a really strong incentive to say that the evidence just wasn’t there. After all, out of 24 cases of extreme brutality referred to the Justice Department for prosecution, 22 were “declined” by the Justice Department.

Last year, Brian Benczkowski, then principal deputy assistant attorney general, explained to Sen. Durbin in a letter that “All of the declinations [to prosecute] resulted from insufficient evidence to warrant criminal prosecution for one or more of the following reasons:  insufficient evidence of criminal conduct, insufficient evidence of the subject’s involvement, insufficient evidence of criminal intent, and low probability of conviction.”

Justice Department employees told Miller of the L.A. Times, meanwhile, that they had “difficulty locating witnesses and identifying documents — such as clinical examinations or autopsies — that could withstand scrutiny in federal court.”

That just doesn’t add up. These were murders and cases of abuse so serious that even Bush officials – who’d been told that waterboarding and the rest of the so-called “extreme interrogation tactics” were legal — referred them to the Department of Justice for prosecution. And they all took place in U.S.-run prisons, with surely more than one lone interrogator present.  (If you imagine the logistics of getting hanging a grown man by his wrists, while they’re tied behind his back, it would seem you’d need at least two people there to do it.)  But there were no witnesses?  No CIA agents or U.S. soldiers or anyone around to see a guy get clubbed to death, or dragged around a floor naked and left in the cold to die?

(This is, by the way, another reason why those photos of torture that the American Civil Liberties Union is still fighting the Justice Department to see, the release of which the Obama administration is asking the Supreme Court to block, are so important – because they’d show some of the witnesses to these crimes.  But I’ll have more on that case later.)

“We wanted to make these cases,” a former Justice official familiar reportedly told the L.A. Times. “We looked at them as hard as we could, and they just weren’t there.”

Holder, to his credit, is apparently not buying that.

Ultimately, any thorough presentation will have to follow the chain of command, and it will be awfully difficult to skirt the issue of waterboarding.

Bruce Fein, a former deputy attorney general under President Ronald Reagan made some really good points about that yesterday on Olney’s show. First, the Constitution says that the president “shall take care that the laws be faithfully executed.” So he doesn’t get to just pick and choose what to prosecute, and not to prosecute obviously illegal conduct. (Fein knows what he’s talking about; as a lawyer in the Office of Legal Counsel in 1972, he participated in drafting impeachment charges against Richard Nixon.) Given that both Obama and Holder have publicly testified that waterboarding is torture and illegal, and given that Cheney has boasted about authorizing it, it would seem pretty clear that something should be done about that.

Fein added that if the president or attorney general don’t want to punish people who may have believed they were following the law, even though they weren’t, then the answer is to pardon them – not to ignore that crimes occurred.

“The reason a pardon is so much more important than no prosecution is that in a pardon situation the recipient confesses that what was done was wrong,” said Fein. “The country doesn’t acknowledge that what was done was legal, but that there are circumstances that justify leniency.”

Clearly, Obama and his attorney general aren’t yet willing to go there. But prosecuting at least the unquestionably illegal activity is a good start.

Stevens, who maintains his innocence, has reportedly not asked for a pardon himself.

It isn’t too shocking that Murkowski — who inherited her Senate seat from her father, Frank Murkowski, when he became governor of Alaska — would ask for a pardon for Stevens. She is part of the state Republican elite that mingles with many of the same mega-donors and special interests, like local rainmaker Bob Penney, who landed Murkowski in the middle of a Senate ethics investigation just a few years ago when news broke that she failed to mention having purchased some choice riverfront property from Penney on her Senate disclosure forms.

Stevens has powerful friends outside of Alaska pushing for him, too. Senate Majority Leader Harry Reid (D-Nev.) said last week that he hopes Stevens is not forced to serve jail time, even though Stevens himself was caught on an FBI wiretap predicting he would be jailed for his behavior.

So far, Bush has been rather frugal in granting pardons. With just 24 hours remaining in his presidency, it will be interesting if he makes an exception for Stevens.

Asked Nov. 18 if [Stevens] would seek a pardon from President George W. Bush, Stevens told reporters at the Capitol, “No, no, no.” But later that day, he explained just as emphatically that all those no’s had really meant “no comment.”

I hadn’t heard that Stevens retracted his “No, no, no” statement, which is different than the non-answer version, “no comment.” It could mean he’s actually thinking it over.

Politico also points out that Stevens’ lawyers sent a letter to the Justice Department claiming prosecutor misconduct, which could translate well into a request for a pardon.

Still, Stevens hasn’t officially asked for a pardon and he has vehemently maintained his innocence. If he does, it’s hard to say how he’d fare for sure, but it looks pretty unlikely.

In his final lame duck days, President Bush has pardoned 14 people and commuted the sentences of another two. That’s the stingiest in recent history presidential history. As I wrote last week, none of the pardoned were Bush loyalists or well-connected Republicans. The most interesting of those pardoned is Leslie O. Collier, convicted of shooting two bald eagles. A grass-roots campaign persuaded Bush to pardon Collier, not ties to the GOP.

But if Stevens gets lucky and his record is cleared, would he run again? Democratic rival Sen. Mark Begich will be up for re-election in 2014, a few weeks before Stevens’ 91st birthday.

It appears the committee may have just stumbled upon a bipartisan solution: pardon Rove.

Rep. Linda Sanchez (D-Calif.) asked Fine whether a pardon of Rove by George W. Bush would preclude Rove from testifying before the committee.

Fine gave her a quizzical look and said he hadn’t considered that hypothetical, but that, no, that shouldn’t prevent him from testifying.

Rep. Darrell Issa (R-Calif.) then pounced on the idea, saying that if all the committee wants is the truth, it should encourage the president to pardon Rove, and then he can talk. He compared a pardon with immunity for a witness who testifies in a criminal trial.

This is probably just a blip on the screen in the ongoing U.S. attorney scandal. But it’s interesting that Issa, a critic of the committee’s investigation, would seek out a pardon of Rove, when the “boy genius” has yet to be charged with a crime (besides contempt of Congress).

It’s also interesting that a presidential pardon of Miers and Rove is in the realm of possibility. Even Ronald Reagan didn’t pardon the key players of Iran-Contra when he left office.