The problem with the argument that Jim is making is that homosexuals represent an extremely tiny percentage of the population. What's more it's not something that is "generally accepted", it's a major political issue in the first world seeing divides of like 50% of the population, and something that is outright detested in the second and third world with the support of homosexuality being one of the things used to rally those people against the first world as being decadent and immoral, indeed one could argue it contributes to a lot of overall political tensions as a lot of countries want to engage in censorship of the media, internet, and other things in part because of this kind of thing and the idealogy the American media presents.
Trying to say that "gay rights" shouldn't be political is by definition a political statement, and a controversial one. Especially seeing as the entire gay rights movement started as saying that someone should not be arrested simply for leading an alternative lifestyle. The very term "alternative lifestyle" has fallen out of use right now, but it was a key element of the whole gay rights movement for a long time. Only some very extreme people were making arguments that gays should be basically inserted into all aspects of society and media, and presented as being around in equal number to heterosexuals and such when they aren't. The movement snowballed into this kind of thing, going to attacks on things like video games for treating an alternative lifestyle as one, and not feeling obligated to include it, when originally it was more based around the idea that what a couple of consenting adults do in their own bedroom is their own business. The whole argument that "it's not like anyone is going to get up in your face about it, if your not in their bedroom why do you care" more or less no longer applies. This is in part why the issue is increasingly political, and why you have a lot of people who were early gay rights supporters now embracing the other side. Even in the US, perhaps the most permissive nation on earth, there isn't real inertia for gay marriage, which is why you see it being passed someplace one day, and then banned another, in part because in order to pass a lot of these laws a political game needs to be played to bypass the normal checks and balances inherent in society to allow changes to laws without the necessary levels of societal support. If there was some trend towards majority or super-majority support you wouldn't see the issues you do now, because a tiny, fringe, minority of haters just couldn't accomplish this much.
What's more, one has to also look at video games in particular and the negative reaction the gay community is getting from it's own actions. Look at say "The Old Republic Online" as an example, a set of designers (Bioware) who showed that they had no problem developing gay and bi-sexual characters when they fit a given storyline, was brutally attacked for writing a game where they didn't insert any such characters and romance options as they didn't think it fit. The basic argument was one of an entitled minority. When Bioware eventually agreed to develop some, a promise it kept with it's first major expansion, the gay community then rallied screaming that it wasn't enough, making it clear (and some people even outright stating) that what they wanted was intrusive gay content, so if you walked onto your ship you'd have homosexuals trying to flirt with you and stuff, with the specific intention of annoying straights in order to make a statement. The clashes over this in and outside of the game have largely died down, but it kind of showed that this is a minority group that tends to escalate it's demands when you give them anything, which can be an issue when your dealing with sexual behavior that actually repels a good amount of the population who aren't wired that way (basically you might not care if two dudes want to get it on, but you don't want to have to watch them make out, or have some dude following you around, trying to get into your pants).
There is also the issue of course of international acceptance, a big question is of course whether a game like a life sim is being intended to be sold internationally and a lot of effort regionally editing it is undesired. Sure the first world might push for their gay relationship simulator being thrown in, but in other countries where such behavior is seriously looked down on or still outright illegal you have a problem. Especially if your heavily selling to various Asian countries who aren't always the most progressive and tolerant guys on the planet. While a nation like Australia might tolerate some easily bypassed filters (South Park's crying Koala) other nations might not be so accepting and it could hurt business relations. While it wasn't sexual I look towards some of the stories I've heard about WoW's release in China, where they have a prohibition against showing the dead/undead walking around, so they had to re-do the entire playable undead faction into something else (basically ugly humans) for a Chinese release which apparently too a lot of work, and lead to certain things playing out very differently since especially early on the major theme is fighting against undead and "The Lich King". Supposedly this also lead to them using less undead in their later expansions (which I haven't played as much) although they were still present as well, and the whole Pandaria thing was in part a compromise by throwing in some eastern (particularly Chinese) inspiration so it could be defended as "mythological" under Chinese law and see less censorship. How true all of this (especially the later parts) are is debatable, but I've run into a lot of references over the years. Surprisingly regional content requirements is something nobody bothers to consider when homosexuality in games come up, it's one case where the cosmopolitan tend to gain major cases of tunnel vision both in the actual numbers involved in their own country, and global attitudes outside of the first world countries the US most shares media coorespondance with.
That said, yes, Nintendo has committed yet another press flub, but at the same time I don't think they can be considered entirely wrong in making their statement about politics. Anyone who has clashed from either side of the gay rights equasion in the USA even and watched the laws waffle, should be painfully aware this is a political battleground even if people wish it wasn't one. Even if a gay-accepting super-majority appears in the first world (as opposed to being wishful thinking people hope will become a reality through claiming it is) it will still remain an international battleground and a factor in anyone wanting to sell a product outside of the most civilized and enlightened countries. Especially seeing as it's not like we're going to start invading nations because they are mean to gay people.
I'll also say that I think "alternative lifestyles" is a slippery slope especially when you start looking around globally. One group that outnumbers homosexuals vastly for example are Polygamists, which can become increasingly common outside of the first world. Even the US has had issues with Polygamist communes and the male children being forced out as soon as legally possible so the older men can monopolize all the girls. I don't know if this game already allows that, but to put things into perspective it could be argued that if your going to allow one alternative lifestyle, you have to allow all of them, especially more common ones, when looking at a global marketplace. Follow that train far enough and even if it's not polygamy and it's problems you will eventually wind up with something that will offend even the most tolerant person. Not an argument I expect to be popular here, but when looking at a product like this it does make a degree of sense to cater to the largest group of people (the supermajority) and pretty much try and omit everything that could cause a serious problem. In absolute terms it's not just gays getting the shaft, it's just that they represent a political flash point in the US and other first world nations. I mean in theory if such nations were more politically powerful in a global scale, you could potentially see some nation that allows and encourages polygamy and has a low age of consent argueing that it's bigoted to have a game based on western American/European standards where they can't say marry 12 year old girls, relegate them to house work once they get "too old" (18 or so) and then marry another one, as a few women's rights coalitions will point out garbage like that still happens throughout a surprising portion of the world, and would count as a valid lifestyle people would want to simulate.
Ahh well, I'm rambling. I'm not going to argue this in detail, I already know most people will disagree with me for one reason or another. I just think it's not that big a deal, and honestly this is probably the wrong place to be trying to draw a line if you support gay rights. It's an easy target from a certain point of view, but really if I was a gay rights supporter I'd be picking other battles, and working more towards trying to create that supermajority as an actual reality than fighting things like this that are likely to just solidify the divide and convince as many people to side against you as they will bring to your side. I'm kind of in the middle of the issue which makes me hated by both sides (strongly pro-gay and strongly anti-gay) so I get it from both ends, which is why I'm not going to bother to get into serious political arguments here again.