No, he was voicing a valid objection to your comparison of people killing in the name of their Gods to people killing in the name of atheism. The two aren't different sides of the same coin. A more valid comparison would have been:
But people kill in the name of their religion often... In the name of irreligion... Not so much.
But people kill in the name of their religion often... In the name of irreligion... Not so much.