There's a lot of people within religions who are gay and may choose to kind of "stick it out" and change beliefs hearts and minds from the inside (See "Dignity", a group for gay Catholics). There's some churches that have splintered off with pretty much the main purpose being to be more welcoming to all (see: Metropolitan Community Churches) But there's also a TON of churches (and there have been going pretty far back) that people just grow up in where it's accepted that Jesus would love him some homogays if he were alive today (see the Quakers).
So, like, your premise is flawed, is part of your answer. Not all of Christianity is "a belief system that produces a strong amount of hate towards something that is seemingly and scientifically natural"
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