I think this scenario is the one that conflicts with canon least. Gene seems to hide personal stuff under his larger than life persona anyway. It's possible that he might hide any tendencies he had from himself (such as in the scene where he says he doesn't have addictions then takes a swig from his flask), but I think he'd probably be aware of them but desperate to hide them. He does seem more anxious than the others about continually reasserting that he's not a poof.

On the other hand, I'm surprised that the usual portrayal of Sam in fic is that he's sexually confident and aware of any proclivities he might have due to being a 21st century man. Sam is an incredibly repressed person and seems uncomfortable with anything to do with sex. If he were gay I'd think it would be very possible for him to hide it from himself entirely.