While it's true that the game doesn't go into details not relevant to the main storyline, I think there's an issue of what Yevon-ism is compared to mainstream religions in this world.

Yevonism isn't a complete religion. It's created by Yunalesca solely as a set of behaviors regarding Sin. Summoners and the pilgrimages, the Aeons and their temples, machina and atonement. Nothing else seems to matter. Since all the murders dealt with in FFX were those of high-ranking clergy members, I keep wondering whether it's the murder that's forbidden, or just the murder of high-ranking Yevonites. So I can very easily see little things like theft and homosexuality not even being mentioned in the teachings, if they don't have anything to do with atonment or defeating Sin.

I definitely agree though about the "I am attracted to a woman" without "I must be a lesbian and will never sleep with men again!" idea, as well as the idea that homophobia isn't just violence and persecution. Adding room for subtlety in both of these areas makes things that much more interesting.