Yes: as far as the German churches, it was a relative handful of people like Dietrich Bonhoeffer who opposed Hitler openly and - to their shame (like the "ordinary" Germans) - Protestant and Roman Catholic clergy/leadership seemed to find it in their interests to either remain silent or even back Hitler.
I think the reason people agree on morality to the extent that they do is that a sense of right and wrong is imprinted in our nature. We are good at ignoring it or making it situational, though. For example, many who commit adultery find all kin...
Your comment deserves a better response than is possible in this forum. I will respectfully point you to Alvin Plantinga's book: "God, Freedom and Evil" as one of the best ways to address this issue.