The people with guns and spies and blackmail and torture devices who are holding captives without trial tell you to do something. Do you honestly think you can say no without risking your neck in some way? Can you get away with dissent in the face of that kind of ruthlessness? Are you willing to bet your life on it?
Basically, you have to be pretty darn devoted to the hypocratic oath to potentially risk your own life for the sake of someone you don't know from another part of the world who is, to the public eye, a "terrorist". And even if you do get away with refusing, odds are very good they'll just get someone else to take your place. It's a pretty shitty position to find yourself in.
If we were talking about the SS instead of the CIA, would we be more forgiving of the doctors for not resisting against coercion? Would we be more willing to realize the danger they would face in doing so, and consequently forgive them their unwillingness to defy the secret police?