William J. Haynes, the Pentagon’s chief legal officer and overseer of Guantanamo’s Military Commissions, is stepping down, amid mounting controversy over the tribunal process, so he can “return to private life,” the Department of Defense announced late on Monday. Haynes’ resignation comes exactly two weeks after landmark charges were brought against six “high-value” Guantanamo detainees.

Haynes “has served the Department of Defense and the nation with distinction,” Defense Secretary Robert Gates said in a statement. But Haynes will leave behind a commissions process that is embattled and discredited–and he bears much of the blame.

Haynes, who is legal counsel for the Pentagon–having served both Donald Rumsfeld and Robert Gates–has long been criticized for his role in crafting the Bush Administration’s policies regarding the interrogation and detention of prisoners captured in the “war on terror.”

His infamous memos and public statements advocated torture and the denial of habeas corpus for detainees. In a 2002 memo, he recommended techniques such as “twenty-hour interrogations, isolation for up to thirty days, deprivation of light and auditory stimuli…and stress positions such as the proposed standing for four hours.” In response to this last technique, Haynes’s boss at the time, then-Secretary of Defense Donald Rumsfeld, wrote in the memo’s margins, “I stand 8-10 hours a day. Why is standing limited to 4 hours.” Haynes also wanted to keep death threats, waterboarding and exposure to extreme temperatures on the table as interrogation methods. He stated, “Fact: The detainees currently held at Guantanamo Bay, Cuba, are not protected by the Geneva Conventions.”

These positions and actions have led to international condemnation and a stalemate in the prosecution of Guantánamo detainees. Only one case–that of Australian David Hicks–has been adjudicated in six years.

Criticism of Haynes has sharpened in the wake of the October resignation of the Chief Prosecutor of Guantánamo’s military commissions, Col. Morris Davis, who charged that Haynes and other political appointees were interfering unlawfully in the process. Davis resigned when Haynes was inserted above him in the chain of command, saying, “Everyone has opinions, but when he was put above me, his opinions become orders.” In a Washington Post op-ed last year, Davis wrote that he had felt pressure to prosecute cases deemed “sexy” in the run-up to the 2008 elections.

And just last week, Col. Davis made the startling claim, in an exclusive interview with The Nation, that Haynes, who oversees both the prosecution and defense, said to him, “We can’t have acquittals, we have to have convictions.” According to Davis, Haynes said, “if we’ve been holding these people for so long, how can we explain letting them get off?”

Reached for comment about Haynes resignation, Col. Davis, who believes that given proper supervision the commissions can be successful, says he’s not celebrating yet. “It’s a positive step, but there are still several people who share his [Haynes’s] views that are still standing in the way of the process,” he said, referring to convening authority Susan Crawford and her legal adviser Brig. Gen. Thomas Hartmann.

Davis has been troubled by the extent of Hartmann’s interference in the prosecution, believing that the prosecutor’s office needs to be independent in order to perform its duties and that the convening authority should be neutral. However, Hartmann, who reports to Haynes, interpreted his duties more broadly, and according to an internal report he “sees the Legal Adviser’s role as being the supervisor of the Chief Prosecutor.”

Lt. Brian Mizer, defense counsel for Salim Hamdan, alleged driver of Osama bin Laden, had a similar reaction to Haynes’s resignation. “It’s an important step in the process in bringing credibility to the military commissions, but it’s going to be insufficient to remove the unlawful influence that Col. Davis has talked about,” said Mizer from his Virginia-based office.

But Mizer is less optimistic about the prospects for a just process in general: “It will never make this system of justice acceptable. We’ve removed fundamental rights that our country was based upon–the right to confront accusers, the right to remain silent, and no amount of resignations are going to cure those aspects of the Military Commissions Act,” he said–referring to the controversial 2006 act of Congress that created the framework for the current commissions system.

The Pentagon’s brief statement left open room for speculation about the reasons for Haynes’s departure.

Col. Davis, who was surprised that such an announcement would come so late in the Administration’s second term, suggested that “there may have been some opportunity that was just too good to pass up.” After the circulation of the press release, it was reported that Haynes will be going to an in-house position at a major corporation.)

As far as Haynes’s future is concerned, there is a possibility that he could be pursued as a perpetrator of war crimes in a foreign country. Indeed, Haynes, along with Rumsfeld, Alberto Gonzales and other Bush Administration appointees, were charged in Germany in 2006 with war crimes, but the charges were withdrawn due to insufficient evidence.

As the tribunals march on, Col. Davis has recently agreed to testify at a pretrial hearing in April for Lt. Commander Mizer’s client Salim Hamdan. Mizer will raise a motion to dismiss charges based on unlawful interference by political appointees, and Davis will be one of his witnesses. He will reiterate claims he made publicly about Crawford’s and Hartmann’s roles in the prosecution.

As Davis puts it, “the house isn’t clean yet.”