It's not a particularly well-known video game, either. It was kind of a dud. Keep in mind, too, that for some other games, it wouldn't make sense to put in homosexual relations. It's not something you should have to force in for the sake of having it.Actually, visibility is LGBT right's greatest ally - so it's actually very important to have representation in media, including video games. I don't know what family values Nintendo chooses to have, but with their public apology, I doubt they care about seeming "safe" to the right-wing crowd.
As for catering to right-wing family values folk, that's what they've always done. They can apologize, but I'd be surprised if you saw any actual changes. They'll probably just skirt around the issue in the future somehow.