It’s rare for a judge to express regret over her own ruling. But that’s what happened Wednesday, when Judge Colleen McMahon of the U.S. District Court for the Southern District of New York reluctantly ruled that the Obama administration does not need to provide public justification for its deadly drone war.

The memos requested by two New York Times reporters and the American Civil Liberties Union, McMahon wrote, “implicate serious issues about the limits on the power of the Executive Branch under the Constitution and laws of the United States, and about whether we are indeed a nation of laws, not of men.” Still, the Freedom of Information Act allows the executive branch to keep many things secret.

In this case, McMahon ruled, the administration’s justifications for the killing of select individuals — including American citizens — without so much as a hearing, constitute an internal “deliberative process” by the government that need not be disclosed.

McMahon did not hide her disappointment. “The Alice-in-Wonderland nature of this pronouncement is not lost on me,” she wrote, “but after careful and extensive consideration, I find myself stuck in a paradoxical situation in which I cannot solve a problem because of contradictory constraints and rules – a veritable Catch-22.” She explained, “I can find no way around the thicket of laws and precedents that effectively allow the Executive Branch of our government to proclaim as perfectly lawful certain actions that seem on their face incompatible with our Constitution and laws, while keeping the reasons for their conclusion a secret.”

The judge’s lament may have, in part, been induced by the striking discord between the looking-glass world in which she found herself, and the hopes that President Barack Obama had first generated for a newly transparent government.

That continued once he was in office. In a Dec. 29, 2009 executive order, Obama said: “Our democratic principles require that the American people be informed of the activities of their government.” He insisted “our nation’s progress depends on the free flow of information both within the government and to the American people.”

He sent an accompanying memo to the heads of all executive branch agencies:

“Transparency promotes accountability and provides information for citizens about what their government is doing. Information maintained by the federal government is a national asset.”

That was before Obama embarked on a secret, exponential expansion of the deadly drone war. Or at least, before most Americans were aware of it.

Since 2009, there have been more than 300 bombings by remote-controlled U.S. drones in Pakistan, Yemen and Somalia. During the entire Bush administration, there were just 51.

Thousands of people have reportedly been killed by the “unmanned aerial vehicles.” Though U.S. officials claim the number of civilian deaths has been minimal, independent studies show otherwise. Ultimately, it’s impossible to know how many people have been killed, or who they were, because the government doesn’t release that information.

This all stands in stark contrast to the heady early days of the Obama presidency.

Back in 2009, overruling the objections of six former CIA directors, Obama released the legal memos created by the Bush administration to justify the use of torture and other “enhanced interrogation techniques” on suspected terrorists.

Today, he insists on hiding memos that justify the secret killing of suspected terrorists – and, as in the case of Anwar al-Awlaki, the killing of their children.

The government has made a point of saying that these killings were all lawful and justified, trotting out senior administration officials to make those claims in a series of speeches over the last two years.

As McMahon noted, “it is not surprising that the government feels somewhat defensive.” After all, “some Americans question the power of the executive to make a unilateral and unreviewable decision to kill an American citizen who is not actively engaged in armed combat operations against this country. Their concern rests on the text of the Constitution and several federal statutes, and is of a piece with concerns harbored by the Framers of our unique form of government.”

The ACLU has already vowed to appeal McMahon’s decision. But its success is far from certain. It’s also unclear whether any court will ever require the government to release the memos documenting its legal rationale for these secret extrajudicial killings. McMahon’s decision, however, highlights why Obama should release them nonetheless.

Demands for the memos have been mounting ever since The New York Times first revealed that administration lawyers had documented their justification for the Awlaki killing in 2010.

Both U.S. citizens and foreign allies, whom the U.S. government strongly relies on in fighting its “war on terror,” have been skeptical of the program’s legality for years. This has stymied intelligence-sharing with foreign governments, such as Germany, and infuriated local populations in Pakistan and Yemen, whose support is critical to defeating Al Qaeda and the Taliban.

It has also undermined Obama’s reputation — making it easier for critics to say he’s no better than his predecessor. It could even tarnish his legacy as a president, for he took office promising shiny reforms after a particularly dark chapter in U.S. history.

McMahon herself noted that there is no reason to believe at this point that releasing the memos would endanger national security, because any “intelligence sources and methods” could be redacted. On the contrary, explaining under what circumstances Washington believes targeted killing would be lawful could both quell critics’ claims of U.S. lawlessness and delineate the rules the United States wants other countries to follow.

To the extent that the memos reflect internal deliberations rather than the administration’s final decisions, the Justice Department can make that clear. Obama can also explain where U.S. policy stands now.

It would be a brave and principled move on Obama’s part. It would also go a long way toward developing global confidence that, despite past mistakes, Washington is waging its fight against terrorism in accordance with the rule of law.

If Obama instead continues to take refuge in the courts, he may be able to claim a minor legal victory. But the president will have lost a far more important battle.

PHOTO: Air Force MQ-1 Predator unmanned aircraft. REUTERS/U.S. Air Force/Lt Col Leslie Pratt/Handout