I suppose I'll have to accept that this is the reason, but I don't think it's that simple. Marriage in the series is definitely an institutional arrangement with the aim of passing on inheritance in the families, just more matriarchal than it would've been in our world historically. With that in mind, I would assume that same-sex relationships would be frowned on. And in the same way, the religious ban surely originates from biology (among other things, I'm sure) and not some peculiar whim of God.
As it is, the Tinkers are the most consistently discriminated group. But if something as boring as red hair can evoke feelings of otherness and prejudice, I would imagine that a different skin colour would do that, too. Maybe RJ could have thrown in a nasty comment from some Tairen merchant who's angry at the Sea Folk for some bargain. Not that I mind the lack of racism.
I think there are many moments of macro-racism (Illianes and Tariens despise one another as do Taraboners and Domani). Cairheinin and Andorans are distrustful ... In fact the only cross national respect we really see is from the Bordelanders, but that probably has to do with the high degree of cultural similarity amongst them, coupled with a common enemy with the blight.
Homosexuality just seems totally unremarkable in the series. Pillow friends and such are taken as a simple matter of course as is lesbianism. Gay males are much more rare, but Algarin clearly inhererted and wasn't considered any less for being gay. Jordan has some peculiar ideas about how being gay works, but he clearly didn't make it any kind of social stigma