In response to the first 2 "counterarguments," almost NO atheist makes these arguments. You're confusing atheism with being an SJW.
In response to the bottom "counterargument," these people weren't necessarily atheist, and the reasons these people tried to get rid of religion was to extend their own power, and they were against religion because they were afraid that it would affect their influence, not because they felt as though the religions were immoral or oppressive or anything.