Even in the military, people are not supposed to follow illegal orders, so they must maintain enough awareness of the situation to evaluate their orders on that basis. I would think that obedience training would be similar - in real life, and not fantasy or stories, one would want to maintain enough sense of the situation and one's own limits to be sure that an order was not "illegal" so to speak. I struggle with this, BTW, because I'm not sure I trust myself enough to monitor properly, so I personally would stay far away from obedience training.