Most killing have been done in the name of political power and economics. War is just politics that has, as Emeril would say, "Kicked up a notch." Religion and other factors are just tools for getting the job done.
The history here is confused. First off, let's put this 'persecution of witches' to rest. People in the 15th and 16th centuries, although Christian, were highly superstitious. This superstition wasn't the fault of Christianity, but simply the *normal human condition* in most pre-modern human societies. Witches were accused of maliciously casting spells and hurting or killing people. People at that time *believed* you could be hurt by a spell. Witches were NOT being punished for being "anti-Christian," but for doing something that practically everyone thought posed an actual, real danger. Look at it in modern terms: the powder sent to the abortion clinics proved to be a hoax, but until it's proven otherwise, people take it as a serious threat. In those days, having no scientific understanding of medicine or physics, they took casting malicious spells to be real. The *intent* was to do evil, in any case, even if spells really didn't work.
As for Joan of Arc, she was a *political prisoner* of the British. The witchcraft charge was a smokescreen, but for the time it made sense - she admitted she heard voices, and wore men's clothing. In those days that was "proof" you were "a witch." Many crazy people were no doubt thought to be witches; again, that showed a lack of scientific understanding.
In the twentieth century, the case is *very* clear that both atheism and paganism have claimed far more lives than any Christian wrongdoing. Atheist Communism was the dominant murderous ideology of the 20th century. Josef Stalin murdered about 9,000,000 peasant farmers (the "kulaks") all over western and southwestern Russia. Mao-Tse-Tung murdered over 10,000,000 Chinese during the "Cultural Revolution" of the 1960s, not to mention the murders of Laotians and Cambodians under communism. The Nazis (who not only murdered 6,000,000 Jews, but another 4 million Christian Europeans, including over half the priests of Poland and many, many Polish Catholics, as well as German Christians who opposed him) were flat-out pagans who made explicit attempts to revive the Norse god worship.
Thank you. It amazes me how some people assume the some total of scientific knowledge and rational thought is the same now as it was 700 years ago. How can the Black Plague be rationalized before the people had any knowledge of microbiology?