Schools are too often the crucible in which social conflicts are fought out, with teachers expected to put right whatever we fail to fix in the world outside. Religion is one such battleground, where “values” are set by education secretaries, and of whom there have been 10 in the past 14 years.

The latest row blew up in Michaela Community school in Brent, north-west London, Katharine Birbalsingh’s notorious free school, regimented to her direction. The discrimination case brought by a Muslim girl last week stirred up rightwing commentators devoted to the headteacher, who made her name condemning education under Labour as “broken”.

One girl praying in the playground soon became 30 pupils, the school says. The KC representing the school trust in the case says they coerced other Muslim pupils to join them: 50% of pupils there are Muslims. “Children were intimidated into greater observance,” he said. “The school observed a child starting to wear a headscarf who had not previously done so. A little girl dropped out of the school choir as she was told by one of the other Muslim children that this was ‘haram’ [forbidden] during Ramadan.” Children were told they were “bad Muslims” if they didn’t pray.

The governors banned “prayer rituals”. A bomb hoax in the school and a stone through a teacher’s window followed a social media campaign and online petition, with teachers intimidated. One pupil was permitted to pray, but was suspended for five days for arguing with a teacher who stopped them bringing a prayer mat into school. The family took the school to court for discrimination. Birbalsingh tweeted: “We believe it is wrong to separate children according to religion or race, and that it is our duty to protect all of our children and provide them with an environment which is free from bullying, intimidation and harassment.” The court will decide soon.

My gut instinct was to back Birbalsingh. If proven true, it’s appalling for children to be bullied into religious observance. As a vice-president of Humanists UK, my hackles rose, as you would expect. By instinct, I like the French revolutionary tradition commanding absolute secularism in schools and state institutions. But French secularism tends to cause less social harmony, not more, used as an easy pretext for far-right anti-Muslim attacks. Humanists defend people’s right to private beliefs and religious practices, as long as they impose on no one else. Yes, I’m sad to see women in hijabs, a “modesty” not imposed on men, but, like Voltaire, I defend to the death their right to wear what they want. Schools navigate competing human rights and cultural demands, warding off protests from ultra-conservative religious parents of many faiths to give pupils good sex and relationships education, including on LGBTQ+ issues.

School heads I asked this week wonder how the situation at Michaela community school reached this state of conflict. “Bullying of any kind has to be stopped at once. This is about bullying, more than religion,” said one. Another secondary head said, “We have students pray at break or lunch, and one of our staff oversees it. Never been a problem. Never heard of it being a problem in another school. If that [bullying or intimidation] happened in my school I’d focus on the ethos and culture where students feel intimidating others is appropriate.”

I don’t know if this explosive conflict is caused by Michaela school’s rigidity, where every minute of every child’s day is regimented: they move silently in single file around the school; while in class their eyes must always fix on the teacher; and there is no free socialising, so in break they only meet in groups of a maximum of four. Before lunch they recite poetry, and lunch conversation is limited to a subject set by a teacher. Parents choose this knowingly, and are rewarded with top exam results, but others would never have their child drilled like this.

How oddly this tale of banned prayers at a non-religious school, lauded by the right, sits in England, where the state pays religions to run a third of our schools – fewer than 1% of those non-Christian. In this most atheist country, pews are empty except when parents get on their knees at admissions time for a vicar’s letter. Why? Because religious schools can select 100% of their pupils, causing social segregation by class and race, as well as faith. They escape other schools’ obligation to prioritise children in care. It’s hard to see what’s “Christian” about that. Faith schools that avoid some chaotic families boast better behaviour and results than neighbouring schools loaded with more than their share of problems.

The Sutton Trust’s alarming report earlier this month revealed just how socially selective faith “comprehensives” have become, even more selective than grammar schools. Top-performing comprehensives admit 5% fewer children on free school meals than would be expected in their local area, and faith schools are most selective of all. Sutton Trust founder Peter Lampl says this “social segregation” is “unacceptable”, calling for a new admissions code. Catholic schools, the most socially segregated of all, always deny it with a slippery claim: “Catholic schools take in 50% more pupils from the most deprived backgrounds than the state sector.” That Jesuitical use of “background” disguises taking socially better-off children from zones marked deprived.

The last time Labour was in power it allowed councils to use lotteries to allocate school places, and 26 councils chose this fairer social spread. But along with scrapping Sure Start and anything of Labour origin, Michael Gove’s great purge during his tenure as education secretary banned admissions lotteries. It’s time to let councils bring them back to prevent social segregation, and time to abolish religious schools.

Polly Toynbee is a Guardian columnist

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