The President is the Commander in Chief of all of the military.The branch that is providing oversight is Congress via funding and in my view has more leverage over this issue than the executive branch. Am I missing something within US politics?
His appointees make up the Secretary of Defense, and Secretary of the Navy...and then it extends on down into the Joint Chiefs.
They have direct command authority over the military.
'nuff said.
This is the way the US Military Command structure is set up and that is the case no matter who is President.
To delve deeper into this set of circumstances though will of necessity get political and on SD we simply are not going to go there.