Well protecting species does probably come natural to most species.
No, generally not. Genes are designed to protect themselves, but this is fundamentally where our fear of "different" comes from. When we see a member of the species that is unlike us, we're pretty hard wired to assume that we don't share genes very closely. It's the foundation of racism, xenophobia, and I'm saying homophobia as well.
What you're proposing is very abstract and intellectual. The idea that our numbers will dwindle if not enough people are making babies is very... mathematic. When we're talking about 2000 years ago, people killed each other... constantly, for very stupid reasons. They didn't care much for the survival of the species if that species was not like them and didn't share their particular social norms.
If Christianity were concerned about the survival of the species, the crusades seems like a bad move. Also... think about the contradiction in saying that a people who believe that God put humanity on earth and has a plan for them are worried about making sure that the species doesn't die off. We're created in God's image, by him, and with his design in mind remember? No need to worry about the species. We're exceptional by design right?
You're acting like religion was created intentionally by atheists... and with the possible exception of Scientology (and maybe Mormonism), I don't think that fits.
That didn't answer any of my questions.
Ok... uh... yes, it's unusual enough (that's one question answered). Are you seriously asking me how prevalent homosexuality is (it has been covered in this thread)? And homosexuality occurs in animals, so I'd say no, not modern. In fact, predates humans seems more appropraite.