The question of "what are you afraid of" stands even in your interpretation. It's tough to say this out loud, but almost every illness is uncomfortable to look at. (Note: the endless debate about whether the "trans illness" is that the body is wrong or that the brain is wrong about the body is not relevant to my point, it suffices only to recognize that something is wrong.)

Lost limbs, burns, skin conditions, non-contagious hacking coughs, every neurological motor disease (which cause strange movements), many sensory conditions (which result in lack of awareness and awkward moments), cognitive conditions which usually result in strange behavior, in one way or another... I have a hard time imagining an illness that would increase people's desire to be around you. The unpleasant reality is that the herd wants to eliminate its weaker members, and we can either embrace that and end up like the Nazis (who exterminated people with physical imperfections and encouraged people who fit their narrowly construed "normal" to breed), or we can resist that part of our nature and be reasonable and kind. Not every part of human nature is good; all evil is done by humans, and everything that humans do is in one way or another a facet of human nature.

There's no clear distinction between the innate desire to get rid of trans people and the innate desire to get rid of anyone who isn't physically or mentally what we're used to, or even the desire to hang around beautiful and intelligent people and leave the ugly ones out. Consequently, it deserves a lot of self-reflective skepticism - because we already know that many of the other behaviors it leads to are harmful even to those who practice them, and beyond that to those who suffer from their practice.

Nobody here wants to “get rid of trans people”, and I think that turn of phrase pretty clearly demonstrates what I’m concerned about. A lot of people have become convinced that, if you don’t agree with their relatively new (and evolving!) ideas about sex and gender, the disagreement by itself constitutes violence against trans people. That mindset seems fundamentally incompatible with academic freedom on gender issues.

I see what you're saying, but "getting rid of trans people," is not an academic issue. It's an issue of whether you invite them to parties, or try to push them out because they make you uncomfortable. We should not let the meta-meta-debate (the debate about whether or not we should be allowed to debate the metaphysical structures of the issue at hand) distract us from the decision we really need to make, which is how to act towards others when they are standing right in front of us.

I really don't know what you mean by "distract" here, because this isn't an issue of some hypothetical in the future. The source article describes a professor who's been analyzing a concrete decision we need to make (what the process should be for legally changing your gender), and protesters who strongly believe that she should not discuss this decision if she doesn't agree with their perspective on it.

Here's what I mean by distract: all of the protesting, all of the comments about the protesting, the entire edifice of cultural activism and reactionary counter-activism, is operating on a level that's totally disconnected from helping anyone.