Terence P. Jeffrey of CNS News has a pretty good article laying out some of the history and background of the decision to try Khalid Sheik Mohammad in civilian court.
Excerpt:
In a May 21 speech at the National Archives, Obama himself said: “Military commissions have a history in the United States dating back to George Washington and the Revolutionary War. They are an appropriate venue for trying detainees for violations of the laws of war. They allow for the protection of sensitive sources and methods of intelligence-gathering; they allow for the safety and security of participants; and for the presentation of evidence gathered from the battlefield that cannot always be effectively presented in federal courts.”