Human beings have never lacked for finding justifications to do the most abhorrent things to one another. Plenty of people have said, and done, horrifying things in the name of their perception of God. And plenty of non-believers have too, for reasons that have nothing to do with religion or spirituality.
You seem focused on this one bee in the bonnet. I see many. Such is life.
I think it would be a curious exercise...and I'm not sure exactly how you could go about gathering the data...to determine just with what - at the heart of it - people have tried to justify "bad behavior." The thing about non-believers, though, is that their non-belief can't really justify anything. Specifically, "atheism" doesnt have any commands. There isn't an edict of atheism that says, "so go break the laws, kill people, etc..., because there is no god." It just says, "I don't believe in a god." What you do from there becomes personal accountability. It means you CAN'T pawn off your values, actions, or morals on anything else but yourself. That's in contrast to a religious person who could say, "look, I'd like to support gay marriage but, hey, the Bible says its wrong and they're going to hell....sorry." That's the distinction of religion: it's spouted as if it's RIGHT and expected to be taken as so, without question, and you can't deny that there is a taboo on calling that out. I can't think of anything else that someone could use to justify evil that is so protected and would be supported by so many.
If one man kills a gay man and says simply, "because I hate those ****," that's not really justification, that's simply the reason, it's personal accountability. If he said, "my dog told me to," that's an attempt at justification, but it'd be dismissed and he'd be wrapped in a white coat and sent away. If he said, "God told me to," that's an attempt at justification, too, and to the point, is a realm many people consider unimpeachable, if not still inadequate. However, realize MANY people agree with that (see my previous link about the preacher who believes the Bible mandates such). Think of the law recently (AZ?) that wants to allow people to discriminate if it is based on your religious beliefs. I feel I should emphasize: There are people that want to be able to MISTREAT certain people, based on whatever, orientation, race, gender - which isn't allowed for any other reason in our legal system - and specifically present their religion as the justification.
OK, to the topic specifically, I encourage OP and others to watch these videos. If you don't think that this conflict is very real, and MATERIAL to this relationship, think again: https://www.youtube.com/watch?v=S1DH3XOK4EI https://www.youtube.com/watch?v=P0AeTV4a_wI
For a freethinker, critical thinker, who has intently come to the state of non-belief in a god, religion, etc..., to embark on a serious, long-term relationship with someone who is embracing (and suddenly so, no less) religion and the beliefs implied therein, is a serious, serious conflict, and should be specifically addressed.