For the record, I wish that more people would, when they feel marginalized, mistreated, or put upon, simply walk away. This solution isn't as good as engaging in civil discourse with whomever propted the feelings initially, but it's a whole heck of a lot better than lighting into a hateful tirade, engaging in personal attacks, or bringing to the gaming table issues best avoided.
While we don't have the full context here, I think that it is entirely possible that the GM here was broaching a subject that would have been better left alone. If there are problems with a player, I generally think that they should be brought up privately. If the GM's remarks were for the benefit of this player, perhaps he should have addressed the issue privately.
He may be homophobic, or he may feel that this player's maturity is such that she will play a character in such a way as to detract from the game.
We just don't know.
Maybe her departure had nothing to do with this guy's remarks. Maybe her pager was on silent and no one noticed that she just got a page from her jerk boyfriend or husband and she was so miffed at being pulled away from the gaming table, she couldn't excuse herself politely.
The issue is intriguing, I admit, but without more information, it's too difficult to make a meaningful inference.
As for whether I've ever had anything like this come up in my games: Sort of. A friend we used to game with once played an extraordinarily effeminate PC. The PC was straight, as I recall, but very effeminate. The funny thing about it, besides the character's wild in-game antics (bard who thought he was a fighter) was that the player is openly gay and not at all effeminate. This guy is one of the most genuinely masculine people I've ever met, but put him in a roll where he's playing a flamer, and wacky hilarity ensues.
) At one point early in the campaign, she attracted the attention of a male noble from another world she was on at the time, who began to try to court her - sending gifts that would arrive at whatever world she happened to be on and so forth. At one point, he even provided material support to the party via the Noble's "Call In A Favor" ability. My character was uncomfortable with his approaches, because she didn't "swing that way", but he was very sweet and kept his distance, and by the time the campaign was over, she was considering marrying him for political reasons. (Her parents were probably going to insist on this at some point with some foreign noble anyway, for their advantage, and so better she at least like the guy. 
)
