You being an atheist really has nothing to do with this. Being offended at how women are objectified/marginalized in the tech industry and being offended at someone's personal religious choice are two completely different things.
Sure and and it makes sense to call Amy from the Python conference in '12 a woman. She is an individual with feelings, hopes and dreams.
But if you want to discuss this issue, you have to do it in aggregate, concerning youself with the average person and what problems she statistically has. Then it makes sense to say female. She isn't a real person, just like no person actually has 2,3 kids.
Also, it's "women", not "females".