The rules are the rules, because the rules are the rules, Mike. Do you not know how to Japan?
This stuff shouldn't be any surprise. Schools were always designed to be robot factories (especially so in Japan). So if they are primarily concerned with imposing order, what relevance does "help students reach their full potential" have to do with anything? That's not order. That's individual flourishing. And individualism to a robot factory means "defect".
Even 12 years ago when I left a teaching job in a private HS in Sapporo, they conducted occasional inspections of boys' and girls' hair. However, certain students were known to have naturally non-black hair, and they were not reprimanded. The others were told to dye their hair back to normal. Case closed.
What I find disturbing about this news story is that the entire school seems to be in on it.
A school representative allegedly told the girl's attorney, "Even if we had a blond foreign exchange student, we would force them to dye their hair black."
Because it would take rebels and visionaries to change it; and they've all been neutered real early by BS like the hair police. Perhaps that's why Japan was such an explosive powerhouse of industry, culture and innovation after the war: the existing hold-you-down power structures had been annihilated, so Akio Morita & Toyoda & crew were unshackled to produce their Walkmans and dominate automotive production etc.
That's why I think opinionated foreigners can actually be useful to the Japanese. Not the grumblers like Debito, but the visionary types. A foreigner can point out stupidity and appeal to reason and a vision for the future much better than a Japanese (since they're all afraid to say something out of place); then all the Japanese can group-reassure-grumble "ohh... that foreigner is behaving strange isn't he...", but at least the idea has been planted in all of their heads. An effective technique on this front is not to say "we (foreigners) do it like this", but to refer back to Japanese from previous decades (e.g. "did Masayoshi Son do as he was told to reach the heights that he did?"); then they can't weasel out of it by saying "that doesn't apply to Japan".