The defense in United States v. al-Nashiri (the next military commission proceeding set to come to trial) has moved for an order (see the second entry under al-Nashiri, # AEO11) obliging the government to declare whether it would continue to hold al-Nashiri in military custody in the event of an acquittal in his military commission proceeding. The short memo supporting the motion criticizes this possibility as making a sham of the trial, but ultimately the main point raised is that the defense needs the information in order to best advise al-Nashiri and to form trial strategy. The defense argues that al-Nashiri is entitled to an answer to this question under the MCA, the Detainee Treatment Act, and the 5th, 6th, and 8th Amendments of the Constitution.
I expect the government will resist the idea that it must tell al-Nashiri now whether it would keep him in military custody following an acquittal, and will certainly deny that any such decision necessarily would require custody for life. Not that I doubt that he would be kept in custody at least for some years following acquittal; an acquittal would prove that the government did not prove beyond a reasonable doubt that al-Nashiri committed a crime, but this does not simultaneously require the conclusion that the government lacks the factual and legal grounds to continue to use military detention. Eligibility for military detention, according to a now-substantial body of habeas caselaw, turns on the preponderance of the evidence standard, as applied to a substantive test inquiring whether the person was a member of al Qaeda at the time of capture. One can satisfy that standard consistent with a military commission acquittal.
In recent decades this has rarely been an issue, since war crime trials like those in the ICTY have been undertaken only after the conflict has ended (at which point, as I noted this morning in relation to Libya, the military detention option already has terminated). But such mid-conflict prosecutions do have a historical pedigree; Ex parte Quirin concerned a mid-conflict prosecution, and the Civil War era saw many commission proceedings prior to Antietam (though many of these, if not most, did not involve Confederate soldiers accused of war crimes). I wonder if there is an example of this situation arising previously. Will post an update if anyone has an example where the issue actually was joined (i.e., an acquittal that required a decision to either release the person or remand them to continued non-criminal custody).