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Did Holder ever say what status he thought Atta (had he survived) and Moussaoui should have?Seems to me there's room to believe he would have simply considered them criminals, because that's the common sense answer.
He was asked specifically about the split in opinion between Rumsfeld and Powell and sided with Rumsfeld, arguing that it was vital that we be able to interrogate them and that "given the way they have conducted themselves," they're not entitled to Geneva Convention protections. He then specifically went on to say that we could hold them for the duration of the war.
He was not advocating that they be treated like common criminals (criminals are incarcerated for a finite sentence, not indefinitely for as long as a war lasts). He was clearly advocating that they are unlawful combatants and therefore not entitled to Genvea protections. He even said, when asked if they could be held "forever": "It seems to me you can think of these people as combatants and we are in the middle of a war."
As combatants in the middle of a war -- not criminals.