I going to go out on a limb and say that the only person that got things right in all this was the guy behind Miiquality: he was polite, non-accusatory, was still willing to give nintendo business and just asked that if it couldn't be fixed to think about it in the future.
The the internet did what it does best and went batshit.
The progressive press ignored any sense of facts to write the usual opinion bits about how wrong it was for the international corporation to not openly affirm gay marriage, and less reputable ones went full out and called them anti-LGBT. The lemming readers, never one to avoid a good twitter shaming of perceived bigotry, didn't stop to ask about context, and went on to vent their usual vitriol about how the rest of the world hasn't come about to the correct way of thinking. People wonder why social justice people get the bad rep, but it's hard to not see spoiled children when your entire argument is "why didn't you think about me you big meanie?)
I mean, I don't think not having gay marriage in tomodachi life is a good thing, but it's a kid friendly, niche title made for a more Japanese audience. It was not likely to be worth the trouble to include it for the NA market given it isn't a high profile, high demand title, and despite what people want, gay marriage is still highly politicized, and not so supported (especially on a global level) as to make those against it a tiny minority to be dismissed. I can't fault Nintendo's decision, though we do need PR people that get that large portions of the internet will throw a tantrum without a lot of provocation and are better prepared to deal with it.