The general model for the "military commissions" law is explicitly given as Court Martial, with some stated exceptions. Obama should have asked Congress to modify the law according to his finer taste, and no doubt the Democratic Congress would have obliged. But he decided in principle to use civilian courts and that was a fundamental mistake.
Report: IDF find M-16 rifle hidden in Palestinian's car in West Bank (Haaretz)
from the article: Report: U.S. trial unlikely for self-proclaimed 9/11 mastermind