My simple man brain is not capable of comprehending why a female protagonist having a partner and expressing affection for them should bother anyone or make anyone feel uncomfortable. I find the idea of female protagonists spending entire games being concerned entirely with grabbing treasure, fighting bad guys and wearing outfits designed to make teenage boys nurse a semi without ever displaying the ability to or desire to engage in a relationship far more troublesome.
I'd wager that half the companies rejecting the game would have picked it up if the main character had a lesbian partner. The whole thing is just stupid. I'd like to think that as a society we'd be mature enough to not be turned off by this kind of thing, but at the same time I can't really disagree with the producers that there probably would be a minority who would have a moan about it.
Either way I'd play the game and I wouldn't give a trout what she did with her romantic interest.