I seriously doubt that any soldier today, would be placing themselves in legal/moral/ethical jeopardy, by following this major’s orders.
That's one of his concerns. If he deployed and carried out his missions, and it later came to light that O was not a legal CinC, all his actions would have been in obedience of an unlawful order. With the US leaning ever closer to participating in international courts, this could very well be a legitimate concern in the next few years. If I were still on active duty, I can't say I'd follow the Major's same course of action, but I certainly understand his concerns.