Personally, I could not possibly care less about this decision. I have no problem with Same-sex relationships in general (hey, your relationship has impact on me, so do whatever you want so long as you leave my relationships alone), so if Nintendo were to have them in the game, I'd applaud that.
However, I can't say I altogether care that they're excluded. At the end of the game, Nintendo is trying to put out a game that reflects the largest audience they can while still being within budgetary and resource concerns. Asking for same-sex relationships to be added during the localization process is not a reasonable request. That's asking NoA to put in the resources to code new content into what already looks to be an extremely text-heavy game. The time to add those relationships wasn't during the NA localization. The time to add it was during the game's original development in Japan, and I believe you already know how little Nintendo corporate cares about Western concerns in game development.
So yeah, it's a pity the option for SS relationships isn't going to be there, and I can understand why those affected would feel excluded by this. I just don't think this was the hill to fight this particular battle on given the resources required to implement it during localization.