The order to report to him, yes, and the other order Lakin is accussed of disobeying. But likely not the deployment order, or even it it came through the Brigage CO, it did not originate with him. Someone gave him the order, and someone else gave that person the order, and so one, until you get to Obama., where as another occupant of the office once said, "The Buck Stops" The question then is "did have the authority to issue such an order?". If he's not eligible, he's not the President, and has no authority at all.
That's irrelevant to the charges. It's the order of the brigade commander he's charged with disobeying and which he'll be tried for.