If the only tool you have is a hammer, everything looks like a nail.
Perhaps we should be satisfied that if we prevent a devastating attack using the President's wartime powers, the legal mopping up operation will be messy. It will not mean that lives weren't saved and that the right thing wasn't done. We are having trouble prosecuting Massouwi, but he didn't get on another airplane.
And I think that's the key point. The purpose here is to impinge or stop an impending attack before it happens. It's sad to say, but our system has always been mostly reactionary rather than proactive...we usually need the crime committed (and its sad results) before we can do anything. While an attempted murder charge is nice...it's nothing compared to a murder charge, which can only happen after someone has died. Heck, other than Visa violations, I don't think there was ever anything we could've convicted the 9/11 terrorists of prior to their attacks. At least this gives us tools to prevent the deaths from occuring.