There are layers of murk beneath the free school and academisation process that would make anybody with any sense avert their eyes. They are too new to make sense of, and too fragmented to see a pattern in. Rumours swirl: of dodgy Ofsteds; academies scoring higher than maintained schools for no determinable reason; and discrimination that, when schools were predominantly under local authority control, would have been so impossible, so laughable, that it's hard to credit.

Many of the problems associated with free schools are related to the fact that they're run by faith organisations. But faith schools have been around for decades without letting in the kind of injustice parents complain of now.

In Derby, a headteacher at a Muslim free school left, complaining, among other things, that girls were being asked to sit at the back of the class. Elsewhere there is talk of discrimination on the basis of caste; documented faith provision that doesn't reflect the local demographic (a Jewish primary school in Wandsworth, a borough that only has 1,600 Jewish constituents in total); communities whose primary schools are being force-academised (this is a word I never expected us to have to make up); parents no longer able to exact any accountability from their local authority and looking around blankly for someone to take their side.

I was never persuaded of what local authorities had done wrong, to be crowbarred out of education. But whatever you think of local authority control, it had pretty good mechanisms for ensuring children received an education without having to make a declaration of belief.

Education professionals have been saying since the coalition came in that it would take years to unpick the damage the free school programme and attendant policies could do. I always thought they meant Toby Young, and shrugged, thinking, he is but one slacker journalist – how dangerous can he be?

But that's not what they meant. Instead, what we're watching is the steady takeover of provision by groups whose influence is the result of something other than majority support. A freedom of information request by the Guardian revealed that 25% of free schools were faith schools. The true figure is higher, since a free school can have a "faith ethos" without being declared a faith school. There is massive variation in how many non-faith pupils a school will take, and the processes are opaque.

Perhaps it doesn't sound all that dramatic, a quarter of new schools being faith-run organisations. But when you consider how many faith schools there were already – 30% – against how many people who say they're religious, this new provision is totally unnecessary.

The problems here are many, some age-old and some a bit startling. We are a largely secular country. Only a third of adults even approve of state funding for faith schools, nearly half actively disapprove, and no more than a quarter of parents would be happy to send their children to a faith school. Well, parents are pragmatic, and there is plenty of expedient religiosity, which then raises accusations about the sharp elbows of the middle classes – an attempt to blame individual parents for a dishonesty that is built into the system. – we are handing over to religious institutions the education of the children of people who don't believe in God.

This is a democratic deficit, before you even directly tackle the Kafkaesque impotence of parents if they happen to disagree with the secretary of state: as atheists and agnostics, we have a right to secular education for our children. Rather than upholding this, the government has removed (democratically elected, accountable) local authorities and thrown open the doors to anyone else who wants to get in. It turns out that faith groups have the foot soldiers, the infrastructure, and the vim to make this happen – what were the chances?

Recent research paints us into a fresh corner, reveals Paul Pettinger, a spokesman for the Accord Coalition, part of the Fair Admissions Campaign. They have no objection in principle to faith involvement in schools, but their research shows that where fair admissions are being compromised, and the school intake does not reflect the social profile of the area, faith schools are the worst – their ranks include 18 of the 20 least representative schools, and 70 of the top 100.

There are schools in that bottom 20 where only 6.3% of the pupils are on free school meals, against 48.7% in the local area. That area, incidentally, is Hammersmith and Fulham, which has a preponderance of highly selective faith schools. The disadvantaged kids there are being systematically concentrated into the remaining, non-faith schools. This is social apartheid – a paradox, given that church schools only sprung up in the first place to educate the children of the poor.

Results like this come up periodically; a trenchant argument against them was launched by Christina Odone in 2008, when she said that religious parents were often eligible for free school meals but didn't claim them, because they had too much dignity. I love that argument, as an insight into the religious mindset ("we're not richer, we're simply better").However, Pettinger says: "The free school meal data was not based on those people who were in receipt of them, but merely those who were entitled to them. So it's an interesting argument, but it's not pertinent."

This debate has been going on for ever. We all pay for schools. On what conceivable grounds should we have to pretend to adhere to a faith we don't have – and maybe receive the Eucharist, or arrange flowers – to get into a school that we've pooled our resources to uphold? But inertia is built into it by history, a sense that just by keeping on keeping on, church schools deserved the educational control they have. What we cannot have envisaged is that a government would airily let this situation worsen.

Twitter: @zoesqwilliams

• This article was amended on 2 October. An earlier version said more than half of the adult population actively disapproved of state funding for faith schools. In fact the survey quoted showed 45% actively disapproved.