Let's start with the idea that civilian trials have too many safeguards and create too big a risk these guys will go free. This does not hold up to any scrutiny for two reasons. First, remember all those high-profile terror prosecutions where the defendants went free? Right, me neither. It just does not happen.
The fact is that federal judges are extremely deferential to the government in terror prosecutions. And national security law already gives the government the ability to do lots of things the government would never be allowed to do in a conventional civilian trial. (People who really think this is an issue seem to base their understanding of federal criminal procedure on watching too many Dirty Harry movies, which, as it happens, I'm actually a big fan of. But remember, they're movies.) KSM is not going to be able to depose or cross-examine CIA Director Leon Panetta or President Bush or Vice President Cheney or anyone else.
Adam Serwer has more:
"They have three sources of authority that would allow him to detain [KSM], one of which is the AUMF [Authorized Use of Military Force], because it directly cites the 9/11 attacks in its language -- the people who planned the 9/11 attacks are combatants and are detainable under the AUMF," explains Ken Gude, a human-rights expert at the Center for American Progress. "Under the .000001 chance that they are acquitted, they will have that authority to detain them."