Gitmo
High-level terrorists needed to be kept someplace under complete U.S. control under top security. If it wasn't Guantanamo, it would have to have been some other military base. This isn't the first example of special circumstances for high-level war criminals. The Nuremberg courts were not civilian either.
A Democratic president who went to war against al Qaeda would most likely have come to the same conclusions.
Low-level criminals and suspects in Iraq and Afghanistan are kept in local prisons, and usually rapidly cycled either for release or further imprisonment.