This is a very thoughtful article!
But I want to quibble with this one characterization. Pronouns are becoming a moral hysteria on the left. The Kiel Area school district didn't have to go all Title IX on the disrespectful students. That's some serious legal firepower to deploy against kids hassling some other kids. They could have treated it like any other issue of classroom bullying. Only if it's a moral outrage do you want to pull out the big guns like Title IX.
Likewise with Nicholas Meriwether. If a professor is disrespectful to their students, universities have ways to deal with that. But unlike other types of being disrespectful, like assigning homework on holidays or belittling students who fail to turn off their cell phones, this one was treated like a Big Deal. (Especially in that Professor Meriwether offered a respectful albeit somewhat irregular alternative--just use the student's name--which was denied.)
Nothing is as enticing to the right-wing manufactured outrage machine as something that the left apparently cares deeply about. To me, the right's adoption of this as a moral hysteria seems largely reactive, mirroring the left's moral hysteria especially since they smell blood here.
I really like how you frame the issues of identity brought up by this. I think you're absolutely correct that this is fundamentally a profound challenge to certain societal assumptions. There's another axis to this you didn't explicitly mention: how important do we consider gender, overall? Although agender (as a subset of non-binary) and trans individuals are put under the same umbrella, I can't imagine two groups with more disparate innate feelings about this.
As you say, respect is an important part of the solution, and tolerance will always be important. But can there even exist a solution that is satisfactory for everyone? How do we balance fundamental incompatibilities?