Court Martial is standard operating procedure for this.
Yes, someone VERY high up is covering things up. Its a REAL SERIOUS problem for the military. There is only a thin veneer of legality covering their asses right now, and it is not real, its only an assumption.
That is BAD BAD BAD. REAL bad.
The problem for Obama with court-martialing this guy is that the moment the court martial begins, Cook gets access to compulsory processes of the court - that is to say, subpoena power.
Not in any command in which I've practices military law would a court martial be a possible outcome for this case. The major was a civilian when he filed his petition for a TRO with the district court. Reservists/Guardsman don't face a court martial proceedings or even an Article 15 hearings for actions that they take while not on active duty.
At worst, the major will face an Army administrative review board if the Army chooses to remove him from the rolls, which is known as an "involuntary separation". He's an officer in the USAR. And, like all officers, he serves at the pleasure of the president. If HQDA decides that a separation is indeed the preferred outcome, he'll be separated without much fanfare. It's a fairly benign and unceremonious event that happens every day in all the branches of service.