We're not comparing the sum total of all possible means by which humans can die, we're comparing ideologies committing willful murder, and more abstractly, theism versus atheism.

Religion has been killing people for thousands of years, whereas Nazism and Communism haven't even existed for centuries.

There is no rational calculus by which one can justify banning Nazi and Communist ideology because of their death tolls and extremism and not also ban the practice of every major religion.