Hmm... Holy Roman Empire (Vigilius onward [538AD], to be kind), The Crusades, The Inquisitions, The Conquistadors, etc... You may omit Europe 1798 (Napoleon abolished papal rule) until 1929 (Mussolini established the Vatican nation) wherein the RCC had limited civil/political influence)... How many would you confess?
No no no, you need to defend your "hundreds of millions" fantasy.
Would you have claimed an even higher number if you thought you could get away with it?
Hmmm. . . . there are a lot of different aspects to this, but I'll try to see if I can make any sense of this.
1. For starters, your claim of "hundreds of millions" is impossible to support. There simply weren't enough people in the world. The explosion in population began in the early 19th Century (there were more people born in the 1800s than in the previous eight centuries combined) and you have already acknowledged that the Church is not accountable for deaths after 1798.
2. Next, it is intellectually dishonest for you to implicate the Catholic Church and not Christianity as a whole for deaths prior to Luther. Unless of course you are suggesting that Christendom should have simply ceded the Holy Land to Islam.
3. The Inquisition is always a popular subject to bring up, but the reality is that most, several thousand were killed (many who were condemned were not even present for their trials and dummies were burned at the stake in their stead). Don't get me wrong, the torture and executions of the Inquisition were reprehensible, but the numbers were not that great. Of a far greater magnitude would be the numbers killed by LUTHER'S followers during the German Peasants' War of 1524-25, these estimates range any where from 100,000 to 300,000 and it was the largest "revolution" in Europe until the French Revolution nearly 300 years later.
4. The majority of wars fought in Europe were between kings, they had almost nothing to do with religion. The only two real exceptions to this would be the French Religious Wars and the Thirty Years War. The French Religious Wars had a death toll of just over 3 million and while both sides were somewhat at fault, I will ackowledge that the Huguenots got the worst of it. The Thirty Years War counted about 7 million deaths which were pretty much evenly divided between Catholics and Protestants and, while the war was nominally about religion, it also was largely political.
I think the biggest thing to realize is that today civilized Christians understand that killing another person in the name of religion is simply wrong. However, the world of five hundred years ago was a very different place. NOBODY valued human life as we do today.