The ACLU lawyers will not contest the guilt of their clients. Rather they will assert that their clients are mentally unfit to be tried because they were "tortured." So the entirety of the trial will be about what was "done to them" by Bush/Cheney et. al. with catastrophic consequences for the defense of the nation (think Abu Ghraib photos on steroids).
But this is what you get when you vote communists into power. As in all democracies the voters get what they deserve.
Problem with your theory is that 9/11 happened before they were water boarded. The 9/11 plans were in place long before Bush was in office. America is on trial, not just Bush and Cheney.