I mean, basically, it comes down to the idea that physical disability should never be a barrier towards being a Starfleet captain, unless anyone is specifically put in danger because of it, because certainly Starfleet has the resources to make it work in some fashion. It's not as if a talented captain who had his or her legs dismembered would ever be told by Starfleet, "Well, our fourth quarter budget projections look bleak, and we're cutting costs left and right, and we just can't afford the bionics for you. Oops." They would just replicate some parts, put an M.D., a few nurses, and a neurobionics expert in a surgery room with the captain for a couple hours and solve the problem. It's a post-scarcity society. If a talented captain happens to come from a planet where everyone is a blob monster, Starfleet would absolutely contribute the resources towards making it easier for them to be the captain.
Essentially, all I'm saying is that in today's society, there's a line to be drawn somewhere where completely integrating absolutely everyone in every conceivable situation is not worth the resources. There is such an abundance of these resources in Star Trek so this line doesn't even matter. Starfleet can absolutely afford to be fully accessible when necessary, except in perhaps extreme, absurd situations ("Well, the captain is made of antimatter, sir. Are you sure it'll be safe!?")
Well, I can't think of a situation so far in Trek where a character was added just so the character can go, "Hey! Check it out! I am a minority!" I think the original goal was a diverse cast that showed people from all walks of life. Poor characterizations of said characters were due to the constraints of having a large cast on episodic TV, not so much the "token minority" effect. Uhura never ran around and exclaimed, "I'm black!" all the time. If we do have characters that are disabled in some way, or gay, or any other minority not shown yet, I have no doubt that the writers are at least self-aware enough to not clumsily write a character in just to be "the gay character" or "the disabled one." We've basically never had that happen. Geordi was in some ways disabled, and his character was multi-dimensional, so there's at least precedent for this to not go awry. As a member of the queer community, I do agree that having token characters is bad. My point is that we've mostly dodged that bullet so far and I don't think the fear of this is warranted.