For NaNoWriMo, I wrote a story that had LGBT characters in it.

It was a fantasy book, set in a sort of medieval-ish era, but I was really struggling with two of the male characters and their development.

One of the male characters (Amalith)was Bi, and had feelings for the two other characters (Thomasyn (male) and Dagmar (female)). He had predominantly physical feelings for Thomasyn, but romantic feelings for Dagmar (with little to no physical feelings).

Dagmar and Thomasyn had this rivalry (Thomasyn's fueled by jealousy over Amalith, and Dagmars fueld by the fact that Thomasyn's uncle is the one that dethroned her father (as well as a subtext of a little bit of jealousy, but she's quite a bit older than Thomasyn, so she was a little more mature about it))

Keep in mind this was a sub-plot that had a little bit to do with the story, but the entire plot didn't revolve around this messy triangle.
I didn't want the primary focus of the characters to be their sexuality. I sort of just wanted it to be a random fact, and Thomasyn and Amalith wind up together in the end (in a weird sort of way), so that's somewhat important because it leads into another story.

I'm afraid I put too much focus on their sexuality and the blatant reversal of gender rolls (Dagmar is masculine through and through, with very few stereotypical female traits) than I did on telling the story.

Even after hitting the minimum word count, I kept writing because the story wasn't finished. I want to continue, but I'm concerned.
I'm afraid that if I ever published it, it might be deemed as derogatory to the LGBTQA community, which is nowhere in the near vicinity of what I meant.

To me, it sounds like a good story. It sounds like something I would read. I don't know what would really make it sound derogatory. Since it's not what you're trying to do. I think that if it's the story you want to write and you can get someone else in the world to like it too then it's worth publishing. The few people that might get offended should not be important. That may sound harsh, but I mean...some people find Harry Potter offensive. If it's going to be like that, why get too caught up in that? Write what you are interested in.