Not really the same thing though is it. The them/they thing is a completely new way of addressing people that doesn't fit with the grammatical patterns we've used our whole lives, so it is awkward and hard to remember.
Really? You've never used They when you don't know gender? This is a standard part of English - feel like I've used that for years. Granted the context around this is different but I wouldn't say it's grammatically new. It's probably easier than remembering a new person's name - shrug, I don't doubt people struggle with it but when I've come across people identifying as they/them, it tends to be memorable enough anyway
Then there's the concern that you'll get castigated if you get it wrong. I'm sure this concern is overblown the vast majority of the time, but it is there. My son, aged 12, got in hot water last school year because he used a classmate's old name, or misgendered them with the wrong pronoun. He swears, and I believe him, that it was completely accidental and he wasn't trying to wind them up (which would be a different scenario). They were talking about an in-school suspension for him, sensitivity training, all this stuff. I was royally pissed off. People can be called whatever they want, I have no problem with that, but you have to be forgiving if people make a mistake or find it difficult to get used to.
It doesn't sound from how you've written it like this sensitity training etc.actually happened?.... and deadnaming is quite a powerful thing - perhaps read up some psychology around the effects of it
https://psychcentral.com/health/deadnamingI'm not saying it wouldn't be better to say Sorry and move on, but perhaps that simply wasn't possible
The misnamed pupil's side is not represented - I can't imagine it's a laugh riot being that age, kids are bastards at that age, not accusing your son at all, but a school taking action at an area of bullying, it isn't hard to see why that's a decent decision.
I can only guess how bad it is to be deadnamed (I have nothing personally to compare it to, like most people I presume), but I think at this point it's probably better to accept for some it is a devastating thing to do.
Accidents happen, but if the pupil was getting it all the time and your son got misblamed... Eh. That happened to me at school loads. It's just the school being, at worst jumpy, but protecting one of their pupils.
So in don't see it as a story in which you were aggrieved (though I can understand that). I see at as a story in which there was defensive action by the school for something I could absolutely see as a horrible area for bullies (and they probably overreacted to your son.)