I want to highlight one other recommendation from the Center from American Progress report on Guantanamo, which I think is seriously worth looking at.
Prosecute 9/11 conspirators in federal court and limit military commissions to battlefield crimes. The prosecution of Khalid Sheik Mohammed and his co-conspirators is the most important of all cases at Guantanamo. U.S. federal criminal courts can handle this prosecution, and it will demonstrate meaningful change, setting the tone for broader U.S. detention policy. It is in the United States’ strategic interest to refrain from seeking the death penalty no matter which forum it chooses, thus denying martyrdom to the 9/11 conspirators. Military commissions remain tainted by Bush-era mistakes, and must be limited—if used at all—to battlefield crimes in order to gain a measure of legitimacy.
Trying the alleged 9/11 conspirators by military commission, or giving them the death penalty if they are convicted would be a supremely bad idea. Because of the more robust military commissions rules, there's little to be gained through trying someone like KSM by military commission -- but a lot of international legitimacy to lose. Why put someone who most people already believe is guilty through a questionable legal proceeding? All that would do is cast doubt on the government's case against him.
Martyrdom is a big part of the Al Qaeda worldview, and granting martyrdom to KSM through execution would merely be giving him what he wants. If he's convicted, let him spend the rest of his life in a cell rather than becoming an inspiration to his comrades.
-- A. Serwer