Here's IRA Steven Behr's take...
“I know they [Paramount Pictures] got a lot of negative feedback, which only goes to prove a point I always believed in, which is that science fiction fans and Star Trek fans are much more conservative than people want to believe, and this whole Gene Roddenberry liberal Humanistic vision is truly not shared by a significant portion of them.”
That might explain why they were hesitant to bring LGBTQ to later Treks. They tried it, they got negative feedback, they decided not to do it again. Even if you don't agree with your viewers' political position, they still pay your salary and you still have to give them what they want.
Precisely. Generally speaking, regardless of the issue, I think social progress is a good thing, so long as you're not doing it just for its own sake. Everyone wants to be fairly treated, and I get that. But in situations like writing a book, stage play, TV show, or movie, you have to bear in mind the responsibility you have to your audience. Sometimes, these situations conflict, and there's no easy answer, which is why treading carefully for both sides is so monumentally important.