While the leaders of the communist movement may have been atheist, such atheism had little or nothing to do with their actions. Their whole purpose was to control the very minds of their subjects. To do this they had to remove any other controlling forces, such as religion. It was greed and the lust for power that drove those men, not atheism. And not science. The only use the communists had for science was in trying to keep up with western advances in armaments.
Can we say the same of those killed for the sake of religions?
An interesting list here, too.