MIAMI – A Pentagon prosecutor swore out new war-crimes charges against three Guantanamo captives on Friday, hours after the Defense Department disclosed that a senior official in charge of detention policy had quit amid mounting criticism.

Charles D. “Cully” Stimson, deputy assistant secretary of defense for detainee affairs, submitted his resignation Thursday, said Pentagon spokesman Bryan Whitman.

Stimson, 43 and a Navy lawyer, had earlier sparked a national legal controversy over comments that cast as dishonorable lawyers who provide free-of-charge legal service to U.S.-held captives at Guantanamo Bay, Cuba.

“The response was not only robust but persistent,” said Whitman. “He had come to the determination that the controversy surrounding him was hampering his ability to be effective in this position.”

No replacement has been named. But the change in leadership comes at a crucial time.

Friday evening, the Pentagon’s war-crimes prosecutor, Air Force Col. Morris Davis, issued new sets of charges against three Guantanamo captives whose earlier cases had been aborted by a U.S. Supreme Court ruling:

• Salim Ahmed Hamdan, 36, a Yemeni who worked as Osama bin Laden’s driver – charged with conspiracy and providing material support for terrorism.

• David Hicks, 31, an Australian who allegedly fought alongside the Taliban – providing material support for terrorism and attempted murder in violation of the law of war.

• Omar Khadr, 19, a Canadian who allegedly tossed a grenade that killed a Special Forces medic in Afghanistan – murder in violation of the law of war, attempted murder in violation of the law of war, conspiracy, providing material support for terrorists, spying.

“We’re going to start with three and add on from there,” said Davis, noting that under new rules for Military Commissions the prosecutors were alleging a new crime – providing material support for terrorism.

The next step is for a supervisor of the Military Commissions process, called The Convening Authority, to look at the charge sheets and decide whether to order trials. She is a former military appeal judge, Susan Crawford, who has yet to take up the position.

Davis’ charges seek to restart a war-crimes tribunal at Guantanamo under new rules and new leadership created under the Military Commissions Act passed by the Republican-controlled Congress during in its dwindling days last year.

But some leading Democrats have pledged to revisit the rules, and the American Bar Association meets in Miami next week, with lawyers debating whether to adopt resolutions on detention policy issues – the trials, Stimson’s remarks and the issue of whether the 395 or so captives at Guantanamo should be allowed to sue for their freedom.

Stimson, a Navy Reserves JAG officer and former federal prosecutor, ignited a national legal controversy on Jan. 11, the fifth anniversary of the establishment of the prison camp, with some broadcast remarks on a Washington, D.C., radio station aimed at federal employees.

Unprompted, during an interview, he recited up a comprehensive list of leading U.S. law firms who let lawyers defend detainees – and said corporate executives “are going to make those law firms choose between representing terrorists or representing reputable firms.”

Legal groups and some newspaper editorials swiftly condemned the comments as being at odds with the bedrock American principle of free or pro-bono representation.

Six days later, Stimson apologized in a three-paragraph letter to The Washington Post, renouncing his own remarks as at odds with his “core values.” He never explained the first statement, nor the retreat.

And, despite a Pentagon disavowal, his behavior became in some legal circles inextricably linked to the ongoing tug of war over the limits of the rights of Guantanamo detainees.

The San Francisco Bar Association asked the state bar to open disciplinary proceedings against Stimson, up to and including being disbarred, because of his position over detention issues.

And Miami defense attorney Neal Sonnett predicted it would be a hot topic at next week’s American Bar Association winter meeting – as well as other detainee rights topics.

Friday night, he said, even Stimson’s resignation would not “quell the interest in the broader issues of due process and fair treatment and the right for detainees to have their day in court.”

On Capitol Hill, meantime, Sen. Patrick Leahy, D-Vt., a lawyer and chairman of the Senate Judiciary Committee, hailed the resignation.

“Mr. Stimson undermined his own effectiveness with his reprehensible comments that showed a lack of commitment to foundational principles of our law and legal system,” said Leahy.