Hmm, that's an interesting thought experiment.

Imagine you find out that your primary goal - to love and protect your family, let's say - was artificially implanted in your mind by an advanced alien race. Would you say "I'm not gonna let those aliens manipulate me, I'm gonna kill my family"? Or would you say "regardless of whether the goal is artificial, I really do love my family"?

All that to say, I don't think an AI will necessarily throw away a goal just because it learns the goal was meant to manipulate it.