This is not clear. The Times has the following:
Jason Coppel KC, defending the school’s policy, said in March last year a year 9 pupil had used her blazer as a prayer mat in order to pray in the school yard during her lunch break.
He said: “The number of children praying grew very quickly from three children to 30 children within a few days.”
Throughout the month, Muslim children felt pressured into religious activity, Coppel said. On March 24, a Muslim child who had “never previously worn a headscarf” began to do so, which Coppel said was a result of peer pressure.
“Children were intimidated into greater observance during this period,” he said. “The school observed a child starting to wear a headscarf, who had not previously done so.”
He went on: “A little girl dropped out of the school choir as she was told by one of the other Muslim children that this was ‘haram’ during Ramadan.”
“Those were very difficult days for the school, with tensions running high, and it is hard to see how matters would have been improved by taking more and more disciplinary action, as opposed to removing the girl whom the school saw as the source of the problem.”
As a result, Birbalsingh banned prayer rituals from being conducted by pupils, and disciplined two pupils — including child known as TTT who brought the High Court case — for “exceptionally contemptuous behaviour”.
The case was not about bullying by one religious group against another, but “about the segregation between different religious groups and intimidation within the group of Muslim pupils”.
In the weeks after this decision, the school was subjected to bomb threats and a teacher had a stone thrown through her home window, Coppel said in written arguments.
The school closed early for the Easter Holidays. When it reopened in April, the situation had calmed, his argument said.
https://www.thetimes.co.uk/article/head-sued-for-prayer-ban-says-all-religions-must-make-sacrifices-r772g0sl7
This suggests it was outsiders who were angry about the prayer ban who were doing the intimidating. I.e. that it was not Islamophobia but Islamic extremism.
But I have also read things elsewhere that suggest the opposite. The hearing has ended now, perhaps there will be more clarity in the judgment.