On the contrary, military trials are military affairs. Military affairs are subordinate to the Executive Branch, per Article II, Section 2 of the U.S. Constitution.
One would have to claim that military tribunals are not military affairs to consistently believe otherwise (i.e., to hold the belief that military tribunals were not subordinate to the Executive Branch), and that begs the question of the very definition of "military"...
The fact that they're military neither means we have to have them nor does it mean they have to be used in some unclear category of cases. Until you decide to move them out of the civilian courts, they aren't involved with the military in any way.