"What I don't agree with is that gender is independent of biology."
This is why I understand "misgendering". Still, I think the debate is different on a societal level as opposed to an individual one. Generally speaking people are healthier if they are allowed to explore their identity with some level of freedom, as opposed to having that identity "imposed" on them. So in that sense I disagree with you that encouraging the "delusion" is more harmful than ignoring it. I could, for example, point to a few cases where men were brought up as women by force and it backfired spectacularly.
Put another way, I can accept that this teacher may not agree that transgenderism is a thing. What I can't accept is that he should have that battle with the child in question.