You think so? I'd disagree, I think it gives the place more depth.
Not to mention people should get over fictional "intolerance", more then enough real stuff like that to get wrapped up in a knot about. Then again that's my perspective and it's one based around the opinion that matters like that shouldn't be crammed into games to begin with. Political statements and satire are fine, but it shouldn't be treated in any serious light.
It's entertainment, nothing more.
Not to mention it's liberating to see it being treated as such; even fairy tales need a bit of moral ambiguity after all.
Well, fiction falls into a realm known as escapism where people immerse themselves into a non-real setting/story as a temporary escape from reality. This realm can also feature unpleasant aspects of reality only it's shown in a way that's easier to see and understand and therefore relate to similar situations in the real world.
But if your fictional story is so "dark, gritty and hopeless" that it's even worst than real life in certain respects then why should anyone care about what happens in said story?
Origins for example features city elves getting abused, murdered, abducted and raped within a system that strips away their identity and forces them into a role of poverty and powerlessness. Any attempt to fight back is crushed and the City Elf Warden would have been imprisoned and executed for having the audacity to fight back if not for the intervention of Duncan.
What stops this from being so dark that your brain tunes out and you stop being invested? The City Elf has a chance to make a difference and while hardship is present, becoming a bann or appointing a bann is a progressive step to giving alienage elves more of a say in their society. It will be hard, but there is still hope.
Same thing with Briala and Inquisition. Having an elf as a high ranking noble over the Dales is just another step to improve the lot of city elves. Again, there will be hardship and opposition, but there is real hope and that's something worth fighting to keep alive.
And believe it or not, this is also reflective of real-life where groups and individuals made substantial efforts to improve the lot of their oppressed minority/socially ostricized group and look at what's happened in the US alone. There's still problems, but there are still clear signs of progress and hope.
As for whether this should be explored in video games, I say why not? Heavy issues are looked at in just about every other medium, why not video games as well?