The key to the gay allegory is to take a much less literal look at it. It’s about representation of a person who is ostracised for reasons related to the broad category of “sex and gender expression”. It is a metaphor, after all, so there’s nothing wrong with being less literal about it.
Speaking of Riker, Jonathan Frakes wanted Soren to be played by a man, to make the message stronger to the contemporary audience. I think the studio chickened out?