If Barry isn't a legal President, by definition he can not give legal orders.
The Nurember trials demonstrated that a defense of "I was only following orders" will not protect you. If the officer knowingly follows illegal orders, he sets himself up for war crimes charges not only in the U.S., but also internationally. It's in his best interest, and his duty, to know that he's following legal orders.
I, wonder, how someone born a subject to the crown of her majesty the Queen of England could be considered a Natural Born Citizen of the U.S.
I don't think this officer's situation would equate to the war crimes trials. Those who participated in the cold-blooded murder of Jews knew it was immoral and ultimately criminal. They knew right from wrong. So, logically "I was just following orders" wasn't a legitimate defense.
If any military officer were brought up on war crimes charges, he would have a legitimate defense of following orders from a POTUS who was elected by majority vote of the electoral college whose election was certified by Congress and who was sworn into office by the Chief Justice of the SCOTUS. Following the orders of a POTUS who turned out to be ineligible isn't clearly immoral (or criminal) if one had no way to know he was ineligible.
Just my opinion. I'm not looking for an argument.