He should only comply to a lawful order. If he feels the order is not lawful, then he has to decide, take a stand and probably have military career ruined, or go with the flow.
From experience though, if a person was to stand up and claim that the order was unlawful, they had better have something in writing to back them up. It can get ugly and you do make those in charge very angry.
Been there, Done that, got the T-shirt.
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Steely Eyed Killer of the Deep