You know ...
I just thought of something that might have been explored as a same-sex relationship for example.
They could do it through the Klingons.
They're a PERFECT example.
Homophobia on a larger scale (but not in all cases) in the real world stems from religion.
Now Klingons were portrayed as a proud, warrior race.
Highly religious and on numerous levels close-minded (or at the very least it takes them a lot of time to open to new ideas).
What if a male-male relationship between 2 Klingons was portrayed which would be highly problematic for a Klingon society to accept.
In essence, have the Klingons portray the same problems with homophobia that exists today, and humans for having to resolve such issues.
Having 2 male Klingons face problems for their relationship could prove to be interesting.
Also you could make it 'universal' by having humans or our heroes in general mention in a conversation how there is a large number of same sex relationships in the Federation and that a lot of those individuals are highly decorated officers for example (if arguing in front of the Klingon court or something they could mention several well known admirals or even captains, perhaps even people who fought against or with Klingons in battle and saved/helped them on numerous occasions) and some of our heroes could be established as being in same sex relationships (after all, no one ever said that all of them were explicitly heterosexual).
I think a Klingon setting for this would be interesting if you want to use aliens to portray current day problems (and not just any 'alien of the week').
But also, that doesn't have to be the main story of the episode.
It could be made in a way that it causes major issues or a large conflict.
My apologies for straying (if it could be considered as such) a bit from the topic.
But I would dare say that there are in fact homosexuals throughout the universe ... or at the very least the Milky Way galaxy where all life was seeded by that first alien race in 'The chase'.
And if that was any indication (along with examples of same sex - albeit solely female type relations - because for some reason it would appear to be more accepted than 2 males
) then it's a trait which is probably shared by most (if not all races in the Milky Way) ... unless some of those races are ultra conservative and resorted to genetic modifications/whatnot to try and eliminate that feature from their population (as distasteful it sounds to me).