Yes, I agree that the submission of his resignation, with the reason for resignation as part of the submission, would have been turned down, but I also agree with P-M that it would have established him as serving under protest for a form of conscientious reason.
There have been other politically based conscientious objection cases, but I’ve not heard of one that ever was approved. Generally, the approved CO cases have to do with the ethics of war or with a religious background (or new faith) of pacifism.
Still, it would have been part of the record.
Is there a reason why the MP’s couldn’t have just taken him into custody as AWOL and put him on a Military Plane to Afghanistan? That would have saved everyone in this matter a whole lot of grief.