Nick Timothy is Director of the New Schools Network and a former Chief of Staff to Theresa May.

“I like the idea of more autonomy for schools,” people often tell me, “but I do have a problem with faith schools.”  After a short pause, they usually go on to say, “well, I don’t really mean faith schools, I mean Muslim schools.”

It’s not difficult to see, given the dangers we face from extremism and radicalisation, why people jump to this conclusion. In the last couple of weeks alone, we have seen a six-year old English child in Luton posing as a jihadist for photographs, apparently in tribute to Jihadi John.  We have learned that more than four hundred children below the age of ten have been referred to Channel, the deradicalisation programme.  And we have read reports that a private Islamic-ethos school in London suspended one of its pupils simply for talking to a student of the opposite sex.

But those who argue that there should be no role for faith and religion in the school system are wrong. For starters, our education system is for historical reasons inextricably linked with religion. Any attempt to disentangle schools from the Church of England – and other churches and faith groups, for that matter – would be a perilous walk through a never-ending legal minefield. An Education Secretary who tried to take the churches out of education would not just be “courageous”, in theYes, Minister sense of the word, he or she would be suicidal. And such an approach would not only be controversial, it would be counter-productive: parents like faith schools and the ethos and high standards they tend to bring. They are significantly more likely to be rated Good or Outstanding by Ofsted, and 1.8 million children – one in four pupils – are educated in them.

“Okay,” some will say, “interfering with the Church of England’s role in education is a legal and logistical nightmare, but do we really want any more faith schools?” But why – since we are now a multi-faith society – should the right to have your children educated in accordance with the values of your faith be limited to some religions and not others? The positive arguments in favour of Anglican and Catholic faith schools apply just as well to those of other religions, too.

There are many good examples of existing faith schools to choose from. Nishkam High School, a Sikh-ethos, multi-faith free school in Birmingham, the Tauheedul Islam Boys’ High School, an Islamic-ethos free school in Blackburn, Krishna Avanti, a Hindu-ethos free school in Harrow, and Alma Primary School, a Jewish-ethos free school in London, are all providing an excellent education for their pupils – and they are all teaching their children how to grow up in accordance with the pluralistic values of modern Britain. Clearly, there should be enough good school places in the local system to ensure that parents who don’t want to send their children to a faith school should not be forced to do so, but that is not an argument against the existence of faith schools.

But what about the minority of people who try to abuse the school system to impose divisive beliefs on impressionable young children? It should go without saying that there need to be strong rules in place to make sure that a school’s curriculum, its uniform, disciplinary and admissions policies are appropriate and in accordance with British values. And there needs to be a structure in place to enforce these rules aggressively and make sure that nobody abuses the trust placed in them by parents and society as a whole.

But let’s remember that the most notorious example in this country of schools being taken over and run by religious hardliners – the Trojan Horse plot in Birmingham – did not involve a single faith school. The schools that were targeted were a mixture of academies and schools maintained by Birmingham City Council. The lessons of the Trojan Horse plot were not, therefore, about the rights and wrongs of faith schools, free schools or academies, but – as Peter Clarke made clear in his report – about poor governance, inadequate Ofsted inspections, and negligence by Birmingham City Council which “failed to intervene appropriately”.

So given that extremist takeovers can take place in schools that are not faith-designated, it would be odd to conclude that in response to Trojan Horse we should clamp down on faith schools. Retreating into an anti-faith mentality would penalise the majority of parents because of the actions of an extremist minority, but it would be a grave error for bigger reasons than that. As the experience of France tells us – which has banned the burqa and bars religion from its schools – aggressive secularism does not work. It goes against the grain of human nature, it makes us less likely to understand one another, and it risks driving certain religious practices underground. If we do not, for example, give parents the chance to educate their children in a school based on their religious values – a state school that can be easily inspected and regulated – they are likely to rely on private schools and supplementary schools which will inevitably be harder to keep tabs on.

But that does not mean the Government cannot do more to use the schools system to fight extremism and promote integration. First, it should encourage the growth of new and existing school chains so schools that are mono-racial and mono-religious because of their geography are incorporated into multi-racial and multi-religious trusts. This would make it easier to get children from different backgrounds in divided communities like Birmingham and Blackburn to mix between schools without having to resort to policies that amount to social engineering.

Second, the Government should create a new category of “need” when it considers new free school applications. This would mean that schools can be established not just when there is “basic need”, caused by a rising school age population, or “educational need”, caused by poor standards in the local area, but where there is “social need”, caused by a lack of social mixing between communities. People who want to set up non-denominational schools or multi-faith schools that bring children together, like the Collective Spirit free school in Oldham for example, perhaps with catchment areas designed to encourage a mix of pupils, should be given permission to open accordingly.

Third, the Government should abolish its admissions rule for faith-designated free schools – which requires a school, when it is over-subscribed, to limit the number of pupils it accepts on the basis of faith to fifty per cent – and replace it with a more effective approach. The existing rule fails according to its own objective: it does little to increase the diversity of Jewish, Muslim, Sikh and Hindu schools, because for now at least they are unlikely to appeal to parents of other faiths. But the rule is effectively discriminatory for Roman Catholics: it prevents them from opening new free schools because it is almost certainly against canon law for a Catholic Bishop to set up a school that turned away Catholic pupils on the basis of their Catholicism. Given that there is growing demand for Roman Catholic schools, which are more likely to be ethnically diverse than other schools, more likely to be in poor areas, more likely to be rated Good or Outstanding by Ofsted, and more likely to provide what parents want, the rule should be replaced by a legal duty on faith schools to ensure that their pupils mix – perhaps through sport, performing arts, or school visits – with children of other backgrounds.

This is a much better approach than trying to close down faith schools, relying on discriminatory admissions rules and ignoring parents’ wishes. We won’t succeed in bringing together our divided communities by pretending to be something we’re not, penalising people for what they believe, or trying to turn others into something they do not want to be. We will bring communities together by encouraging people, especially young people, to understand, respect and like one another for what they are. So next time there is a debate about how to tackle extremism and there are calls to push faith into the margins – whether it is in schools, society or in public life – we should resist those calls and do what conservatives always do. Instead of trying to re-make man in an unrealistic, idealised image, we should be pragmatic and go with the grain of human nature.