Faith Schools (which are at least partially funded by private benefactors) are perfectly entitled to teach whatever woo they want. Creationism is taught at some of these schools as fact, and there is nothing that can be done about it.
The schools involved in this story are not faith schools. The teaching of religion is not against the law, although these are secular schools by design. What appears to have happened, however, is that key figures in the governing bodies and classroom have been hounded out and replaced with more ardent followers of islam. Again, for clarity, these schools are in areas of England where the student population is 80-90% muslim. Staff at such schools would be expected to mirror the local population to some extent.
Where this story becomes unpalatable is that the very fabric of the schools becomes subjected to a kind of enforced islam. Women teachers are harassed, female students are forced to sit at the back of classes, various unfair-dismissals alleged. Stealth and suspicion abound. All the kind of shite that you would expect. Evidence of wrong-doing is scarce at this point though, and the Trojan Horse letter itself is thought to be a fake, written to highlight a perceived problem.
Here's the twist. If the schools were renamed Faith Schools? Move along, nothing to see here. We, the viewing public, are supposed to be outraged by the religious side of the story, but really it is just a funding dispute. The Gov funds both types of schools, to greater or lesser degrees, and is really being forced to act because it isn't getting the type of school it is paying for. Very little of this is actually about religion, and whilst these schools certainly do have problems, the media are certainly getting their money's worth.
Similar, though maybe smaller scale, gerrymandering / nepotism / religion-based bigotry exists in C of E schools, for example, but it is done by white ppl drinking a cuppa tea, so it is completely ignored. Whilst any plot, if proven, would be a serious breech of rules and would cause heads to roll, this story really just highlights how non-muslim britain views islam.
Written for context only, I am in no way supporting what may or may not has happened here. Woo-peddling to kids is woo-peddling to kids, whatever flavour of woo, or indeed kid, you choose.