The Vatican started by killing every single pagan and gnostic in Europe.

Even if I grant you that, why would that be wrong in your worldview? Didn't the pagans wantonly kill Christians and jews in Roman times? How can you claim "Vatican bad" when you don't have a standard for good? Show me one non-Christian state in history, where people of convictions opposite to the status quo weren't prosecuted. Because it seems to me your beef is not with religion at all but with human nature which always seeks to eradicate ideologies perceived as threatening the one in power. Since you're an atheist why do you consider it wrong that the more powerful oppresses the less powerful? Isn't that what nature is about?