Let's cash this out a little bit - Which was worse, the heresy prosecutions of the Medieval era, or the Cultural Revolution? I think the answer is the Cultural Revolution, if for no other reason than more people were affected per year.
But that's based on technological improvement between the two time periods:
Once we control for those effects, I think it is hard to say which is worse.
In contrast, I think the social changes that led to the end of serious calls for Crusades were a net improvement on human, and I'm somewhat doubtful that technological changes drove those changes (what probably did drive them was that overarching unifying forces like the Papacy lost their legitimacy and power to compel large portions of society). Which isn't to say that technology doesn't drive social change (consider the relationship between modern women's liberation and the development of reliable chemical birth control).
As a percentage of total planetary population, a large number of historical wars were worse than any 20th century atrocity. Pinker has a list in his book, and there are enough that they include wars most modern people have barely heard of.
Here's the new thread for posting quotes, with the usual rules: