Well, It'll affect sales, there will probably be an outcry, but I dont think it'll be a massive uproar, as I have never heard of a game in the past that has homosexuality, I know theres a game with Lesbian characters ( forget its name ). It depends on how far they take it, if there is a male to male kiss, I'd say it would be an uproar.
I think it will affect sales IMO, thats why they wont do it.