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Actually, sloppy thinking is when you decide about all prisoners taken based on their affiliation - viz. al Qaeda. If a prisoner is a civilian, and is taken in the war zone, and is a citizen there, they are entitled to GC4 protections. If they are a combatant, to GC3 protections. Exactly what protections are to be determined by an Article 5 hearing. Before that hearing is held, or if it is not held, they are afforded treatment due to either civilians or to prisoners of war.
A prisoner taken not on the battlefield, not in the war zone, not fighting, is not a GC issue. Such a prisoner has to be charged with a crime, they have to be extradited, and they cannot be held under GC for the "duration of conflict". BTW, that last situation applies to Khalid Sheikh Mohammad, who was captured in an apartment in Karachi, and is a Pakistani citizen.
If the U.S. wants to conjure a circumstance where he is a war prisoner, he becomes a civilian, in which case his deportation is illegal, and his status for release needs to be evaluated every 6 months. Declaring someone whatever is convenient to evade the law is not legal behavior on behalf of the U.S. government.
I get fairly upset when I think of KSM, because he was talking before the torture to FBI agents, and a squeaky clean case could have been built and brought against him with an iron clad conviction.