In our justice system, we presume innocence. That is not true in most other countries (witness the outrage when an Italian court convicted an American citizen using Italian standards of justice). We also allow a variety of defenses against charges of murder even when it is clear that the individual involved actually committed the act for which he is accused. Thus, Roeder -- a terrorist nutjob -- could have entered a plea of not guilty by reason if insanity rather than justified homicide. I suspect that a similar claim of reduced responsibility could apply in the case of some small children that could be used as walking bombs by terrorist groups.
For what it's worth, trying a person in a military tribunal does not change the standards of due process, only the procedures in use. Similarly, holding the trial outside of the country but under American control also does not reduce the rights of defendants and was decided by the courts over the objections of the Bush administration.