Firstly, I'm sorry to hear that your son has fallen foul of the system in this case. That must be a hard situation for all concerned.
I take your point regarding the establishment, and it's failures, I'm sure that is a driver for social division. But the educational establishment specifically, no I don't see that. Not unless it's changed significantly since I was in it. Though I do admit, I wasn't remotely interested in politics as a child, or even a young adult. I don't believe that I was atypical in that. So it's hard to see exactly how much influence schools and universities actually exert, if most of their fodder is not politically minded at all. Hands up anyone who took any notice of all the political shenanigans in their young years?
Are you sure about those Prevent figures? I'm not. I tried to have a similar discussion with Johnsond on this subject last year, to no avail. Shortly after the latest Prevent report had come out. I'll see if I can find it if I get some time. The largest type of referrals is for individuals judged to have no identified ideology, not RW.
Personally, I'm glad that schools take the matter of radicalisation, of any persuasion, seriously. It's obviously far from ideal, but I'd rather that they be over cautious, than miss stuff that later turns out to be a problem. (Not applicable in your case obviously, so not a consolation. I don't know the details of course, nor would I wish to discuss them on an open forum.)
Thinking about it some more though, in most of the recent high profile case, with tragic consequences, it's the Prevent program that's been at fault. They've missed things, or not acted on information that's been passed to them by other agencies or institutions. That's what happened with the Southport attack, and I'm sure some more that've made the headlines for plotting or actually carrying out awful attacks. That youth in Luton, Nicholas Prosper, wasn't even flagged on the system. It was only through luck that he didn't claim far more young victims. In some ways kids like these, with no identified ideology, but just a sick fascination with extreme violence are more of a concern, hinting at deeper societal problems. Which links back to the point about the deluge of unregulated extreme content on social media. Not to mention the numerous attacks driven by extreme Islamic ideology.
So yeah, more clearly needs to be done on this issue. Probably not by schools, but certainly by Prevent and similar intelligence agencies and also some attempt at online content regulation. Even, dare I say it, parents should take more responsibility over the behaviours of their children. Too much is shirked and pushed onto schools these days, as I think you agree.