Agreed, but that doesn't mean the crew are guilty. They are given orders from elsewhere and are not concerned with geopolitical problems. Their job is to defend the nation, they have no idea as to what is or has occurred off of the ship, and they don't evaluate what they are told unless they have absolute proof. Someone above broke trust.
Years ago I read an article that the CIA was using forest service aircraft for operations in Australia, I believe they have a very limited budget hence the black ops. And Q said CoC, Chain of Command. I don't think the crew is rogue, it sounds like they were given bad orders.