There were resistance movements, some of which got quite famous. Most well-known to me would be Dietrich Bonhoeffer, a Lutheran theologian who was quite vocal about his opposition to the Nazi regime and eventually participated in plans to assassinate Hitler. It failed, as we know, and he was sentenced to death for his role. He very much grappled with the question of whether murdering a tyrant was a sin, but eventually came to the conclusion that it had to be done either way.

He also petitioned the allies to differentiate between Germans and Nazis once the war was over, pertinent to your post.