Just report abuse/insults, block the person and move on once the discourse has gotten to this point. Past a certain point of hostility you can't really have constructive discourse with someone. Discourse can only really happen when both sides believe something productive can come from interacting with each other.
As an aside: trans and genderbend fetish stuff has always been... mm... I won't say intimately connected? But whether trans-hostile gender-bender fans like or not they're definitely adjacent. For instance the person who made the anime girl genderbend plague inc mode came out as trans a while ago.
It's good to know that I've had a positive presence on MD's genderbend comment sections though! I've been trying to be less overtly combative but still engender a positive atmosphere for people who like fluffy stuff and decent stories as well as fun kinky times. I think this is our time.
And yeah, back on topic -- I do really feel bad for Minami here from a trans-interpretive version of this story. I actually agree with people who'd say this manga's "trans energy" isn't necessarily intentional on the part of the author but... well... death of the author is in play. If "Magical Trans!" is meaningful to you that way, it's meaningful that way period. It's inherently valid. And yeah, in that light, I think it makes sense to feel bad for Minami here.