I meant to add, I wonder if in any event the courts should intrude into the command structure and process in the military as a matter of policy? Should a service member be able to go into court for extraordinary relief in the form of an injunction against the enforcement of an order? What about going in simply for relief like a declaratory judgment on the validity of any random order? I hope the answer is no.
One aspect of every briefing given every member of the military is that one must always disobey an unlawful order. That's codified, but one also must be damned sure about it before one pulls that rabbit out of a hat. The consequences of a misread would be prison.
That's within the military system, however. One doesn't take even that to a civilian court. At the same time, there are many issues (divorce, for example) that JAG doesn't handle, which, when they arise, the military member is pointed to a civil court.
Questioning the legitimacy of an order from the Commander in Chief would seem to me to fall into the military court system and not the civil...IF this non-lawyer were asked to guess.