I think that's an overreaction. If you've studied any psychology, it becomes very clear that obedience is hard to break out of for most of humanity, even if the person doesn't agree with what they're doing. Have you ever heard of Stanley Milgram's experiment? 65% followed through with the entire experiment (meaning they gave what they believed to be lethal amounts of electric shock to the "learner") despite not agreeing with what they were doing.
I'm in no way agreeing with the Nuremberg defense, but the power of obedience and authority is very real.
As for Christianity, most of the followers are good people who are simply trying to live their life by their belief of God, which is completely praise-worthy. The problem is that Christianity is vague enough that it's easy to corrupt or twist to one's own personal beliefs or agenda. No other religion in history has as many offshoots and sects as Christianity.
Unfortunately, the fully commendable amount of religious zeal found in Christianity can be a double-edged sword as some people can be swayed off the course. Religion should never be a tool used to accomplish some earthy gain. If you don't like the way someone lives then don't associate with them.