It's interesting that the writers added that bit of dialogue.
Sure, to any Bond fan, it'd be easy to spot that as a nod to CASINO ROYALE. However, to the average theater goer, or even a person seeing a Bond film for the first time, they'd go ahead and think Bond is bisexual, or that he was hinting at some past homosexual relationship.
However, I think that SKYFALL is for Bond fans, first and foremost. A lot of the material in the film reference the Bond films of the past. For example, you wouldn't pick up on the Aston Martin humor if you didn't see GOLDFINGER. I don't think they're paving the way for a gay Bond. Not yet, at least.
GayQ, on the other hand...