The only thought i have on this is that it's annoying this is even considered news. I mean, it hardly matters (would just like to say, this is not aimed at you, more at sites like Kotaku that feel the need to report this).
I'll be honest, i'm not a big fan of homosexuals, i don't mind them but i have no intrest in what they get up to. For a game to handle homosexuality correctly, it should not even come up if you play it as a hetrosexual. Likewise, if you would like to play as a homosexual, there should be no reprecussions, or indeed any prejudice against it.
On the subject of another game (Mass Effect 3), i'm slightly worried that Shepard has all of a sudden decided he likes abit of bratwurst. It just seems so out of character for a character that hasn't shown any homosexual tendacies to this point (unless you count blue alien's as lesbians of course).
But that's a topic for another thread.
Basically, just make sure it's natural, rather than having overly flamboyant boys prancing around like twats.