Hate to be lawyerly here, but the purpose of a criminal trial is not to exact revenge on a person for their evil associations, but to prove, beyond a reasonable doubt, that they committed a crime. Then, to affix punishment. I don't know the whole of the complaint against the little Muhammad here (I think he actually pleaded guilty and the jury was just there to decide die or no), but mostly what I heard about was about whether his failure to tell the FBI about 9/11 was the proximate cause of it. In a civilian context, that would be very weak indeed.
My own view is that this didn't belong in a civilian court to begin with. A military determination that he was 1) not a citizen of our country and 2) a member of AQ is enough for a cigarette and bullet, period.
By the standard we applied to Mouse-awee, if one million Red Chinese paratrooped in tomorrow, each and every one would be entitled to a full-dress trial, one at a time.