The Barack Obama administration’s decision to try Khalid Sheikh Mohammed, the self-proclaimed mastermind of the Sept. 11 attacks, and four other al-Qaeda members in a military tribunal has left plenty of Americans unhappy.

Civil-liberties advocates say the commissions lack legitimacy. Many New Yorkers feel cheated of a chance to dispense justice for a devastating assault on their community.

Still, the White House made the right call. A criminal case in Manhattan would have necessitated Congress ending its effective ban on moving prisoners from Guantanamo Bay, Cuba, into the U.S., which is highly unlikely. It would also have been enormously expensive and a security nightmare. A military tribunal is far preferable to no trial at all.

More generally, critics of the tribunals tend to ignore the many significant improvements to the system made since 2006, when the Supreme Court found that the commissions created by President George W. Bush were in violation of both the Geneva Conventions and the Uniform Code of Military Justice. Among other changes, commissions now exclude any confessions obtained through torture, degrading treatment or other coercion; they use virtually the same rules for dealing with classified evidence as a civilian court; they now allow detainees more freedom to choose their own attorneys; defendants have the right to appeal all the way to the Supreme Court. Surprisingly, many experts think that the sentences meted out in seven convictions reached so far have been lighter than what the defendants might have expected in federal court.

Yes, commissions differ from criminal trials in some significant ways: hearsay evidence is allowed (although rules allowing it have been made far stricter) and there is no jury. But, all in all, Attorney General Eric Holder was correct in saying that “the reformed Commissions draw from the same fundamental protections of a fair trial that underlie our civilian courts.”

Indeed, Mohammed’s repeated admissions that he planned the attacks will probably be excluded as evidence, because he was repeatedly waterboarded. Rather, the prosecution is expected to make use of testimony from Majid Khan, an al-Qaeda operative who attended a Maryland high school and reached a plea agreement with military prosecutors in February. The Khan deal was one in a series of triumphs for Guantanamo’s chief prosecutor, Brigadier General Mark Martins, who has also wisely created venues for victims and journalists to watch the proceedings on closed-circuit TV and put transcripts online.

The system could use more refining. We would like to see the White House elucidate the criteria it uses in deciding whether suspects will be sent to tribunals or civilian trials or are to be held indefinitely. We also want the prison at Guantanamo shut down, which means Congress has to give up its collective not-in-my-backyard mindset and find a domestic location for internment. Shuttering Gitmo would help convince skeptics that the U.S. is committed to the rule of law in its struggle against global terrorism. So, too, will a fair and open military trial of Khalid Sheikh Mohammed.

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