I've got a feeling this has more to do with Japan's marriage laws being behind the times than Nintendo trying to make a statement. Of course that doesn't make it right, but it explains it.
I feel like you missed some vital information in this one, Jim, like the effect that the glitch had on games and the fact that the game couldn't be changed for an English release, but your point still stands: homosexuality should not be a taboo topic. It should just be a thing.
I have a feeling that part of the reason Nintendo felt this was the "safe" decision is because the game is rated E for Everyone. I'm a progressive individual, but cynicism leads me to believe that with the current (unnecessary) politics surrounding same-sex marriage, that the ESRB and other rating boards would bump the rating up for having homosexual relationships at all. Again, that's fucking stupid and doesn't justify it, but it should explain it. Perhaps the reason we don't see controversy like this with the Sims or Skyrim is because they're rated T and M respectively...? After all, you see gay characters all the time on more adult-oriented TV shows, but god forbid our precious children are exposed to the gay! They might start exercising tolerance at a young age, or willingly sell the sodomites goods and services in exchange for currency as if they were... *Gasp*... NORMAL PEOPLE WITH DIFFERENT SEXUAL ORIENTATIONS! Gay children will get it into their heads that their sexuality is nothing to be ashamed of, and before, THEY'LL BE EQUAL MEMBERS OF SOCIETY! ORPHANS WILL BE ADOPTED AND TAKEN OUT OF A BROKEN FOSTER SYSTEM, AND TEEN SUICIDE RATES WILL PLUMMET!