Right, they have the power to do that, and yet obviously Congress does not decide EVERY SINGLE POLICY in the military, as that would be impossible, wrong, and stupid. I say just let the military decide their own sexuality policy and leave it be. If you have a problem with it, try and change the minds of the Generals etc.
Civilians do ultimately control the military but their internal affairs should be handled... internally, within reason.
Regulating the military is one of Congress’ enumerated powers. You want to dump part of the Constitution?