I tend to get the feeling that you want the FFXIV team to take a stance regardless of what the parent company as a whole, the board of directors, the shareholders, other companies, as well as any partner organizations, as well as other players in differing country markets desire.
Sure it's a few lines of code to make it happen, but it's the stance behind it that's what is keeping the team from doing so. I'm sure that if Yoshi-P and team could just slip those few lines of code in and things just so happened to remain quiet, they'd do so. But we all know that there would be multiple articles published about it -- to agree or disagree with the decision. That single decision would get loud. All across the spectrum, it'd be a thing to be heard about. Look at the press that BioWare got from the Dragon Age and Mass Effect games. And then SE has to deal with the fact that they just jumped into a political issue and took any sort of stance. If they do it, it's going to hit the media in some form or fashion. The spot-light is going to be on them and they'll have to make statements.
I'm sure that the company wants to be as non-involved as it can be when it comes to things because they have to consider their financial impact as well. As I said earlier, it's not as simple as popping in a few lines of code. There are multiple things to consider with this entire situation. Personally, I have no issues with same-sex marriage in the slightest, but SE isn't in a predicament to take a political stance on this and it's likely coming from the top of the ladder, down.
It's not that they don't support it, it's that they have to consider any and all financial repercussions that would come with taking a hard stance. You have to consider the business aspect of this. If you're just thinking that they're doing it because they want to be unfair, then I'd wager you're very much mistaken in that aspect. Consider their position as a business, their country of origin, the values in that country, as well as their financial situations as of recently, then you would likely consider "why" they're trying to be as hands off as possible.
As a Japanese software company, the last thing they want to do is to throw a wrench into their finances because they are leading a charge on a topic hotly debated in politics. They just want to make software and distribute it to as many consumers as possible. I'm sure they're not trying to be a trailblazer on anything aside from that.
Which, again, is why I am for scrapping the whole thing. Or, they could do as some others have said here, just implement the pieces and let the players do as they will. On that, I can agree is the safest. Again, I don't believe it's that they don't support anything, it's that they can't get involved for fear of jeopardizing their income as a company.