It depends which way you look at it, (and granted Sulu is an exception) but generally the episodes which feature non-straight characters end with prejudice being the winners. In those episodes which specifically try and explore ideas of homo/bi/asexuality and, or trans/intersex:
-In The Outcast, despite Soren's plea to be allowed to adhere to her biological gender, "What I need, and what all of those who are like me need, is your understanding. And your compassion. We have not injured you in any way. And yet we are scorned and attacked. And all because we are different", she is still forced to comply to societies norms/fears/prejudices.
-Rejoined treats the love between two female characters as forbidden and punishable by exile.
-Profit and Lace considers gender reassignment surgery, something many people have to wait years and jump through hoops to have, as immaterial as just changing clothes.
-The Emporer's New Cloak features a lesbian kiss between characters specifically labelled as morally corrupt.
Though prejudice wins in "The Outcast" and "Rejoined", I think it's crucial that these are not portrayed as good outcomes. They are defeats for our characters, and defeats for the values the show is espousing. "Rejoined" I think is actually devastating in it's conclusion (and "The Outcast" has some impact, I take issue with that episode in other ways).
You won't get any argument from me on "Profit & Lace" or sexuality in the MU, though. Highly problematic all around. "Crossover" manages to make it work, basically just on the strength of how fully realized Nana Visitor's performance is as the Intendant, and then it's a slow degeneration from there, getting increasingly offensive each time we go back...