So, if you are really looking at long bloody history and choosing between atheism and Catholicism
If that were what I were basing my decision on, then it would be relevant. I'm not. Humans are as they are, and Christians are no better than the rest. Christian institutions have instigated a lot of bloody death. This is only more elevated because it claims to carry a message of love, and it certainly does not at all times. Individuals vary of course. I actually don't need to own Pol Pot, because I have nothing to do with him, his ideology, or his morals. He was a free agent, and a monster. Since I belong to no organization that condoned his behavior, I feel pretty removed morally from his atrocities.
There is nothing about atheism that demands any actions whatsoever. We only agree that there is no evidence for a god. We don't go to services that preach Inquisition, Crusades and witch burnings. MOST people don't go to such services today---but that is the history.
Now on to what I based my decision on. If I believed in a god, and I believed it was working through the Catholic church, then I would not be deciding between atheism and Catholicism. I would be a believer. I would not suddenly be an atheist because of the behavior of that church or some of its people. I would not suddenly be a believer because of wonderful things attributed to that church and it's people. The actions of people don't really define the issue for me. It is evidence, but not the deciding factor.
I find no evidence for that god. Not personally, not in nature, not in the behavior of the people or institutions. That makes me an atheist. If a Catholic nun found me beaten and broken on the street and took me in and made me well and comforted me, she would be a wonderful person. But that would not make me Catholic, because that does not address the only issue that matters to an atheist when making such decisions----is there a god. I know that if an atheist, Buddhist, Wiccan, Jew, Muslim, or Hindu found me in the same condition, they would be just as likely to help (if not held back by prejudice). Because that is part of the human spectrum. Some from all groups may also pass me by. Another end of the human spectrum.
The thing that angers me is when an institution says it is representing a god of love, but when it gets some power it uses it to do a lot of harm. Perhaps the issue is power. We just shouldn't let them get too powerful, while at the same time protecting their rights to exist.