Up until now I cannot say I have been overly concerned with female vicars. That one in Dibley seems fun but mostly I am with Bill Hicks: "Women priests. Great, great. Now there's priests of both sexes I don't listen to." I don't believe or even pretend to believe in order to get my kids into the right schools.

Nor am I under illusion that the Church of England is some hippy-dippy hirsute cerebral force for good. Bits of it may well be. When I lived in London's King's Cross, the local vicar – "Trev the Rev", as he was known – let the prostitutes sleep in the church when they were under assault from vicious punters and the police. This seemed to me a fine Christian thing to do. But for every Trev the Rev there is some reactionary gittish vicar determined to keep up the fine traditions of homophobia and misogyny.

Unity in the church is a joke. When I asked my local vicar if I could use his church for a blessing ceremony using a female Baptist minister, he made clear his feelings about women vicars. But half a mile up the road the clergy were in the middle of a big gay picnic and had no problem with anyone using their building. For a donation. Which is fair enough.

One encounters these inner-city vicars who don't seem to mind what you believe – some will even say that the resurrection is but a metaphor – but don't be fooled. At the heart of the church is a steely core of evangelicals who have far more say than they should. The provisional wing of the CofE is as fundamentalist as they come: the one thing that all fundamentalisms share is the need to keep women in their place.

Thus we had the farce of the vote against women bishops when there have been women priests for 20 years, which the majority of the congregation accepts. To ban those women from promotion is discrimination that would not be acceptable in any other walk of life. The church, with its mystifying voting process, looks not only archaic but also impotent as the vast majority of the synod did not want this result. They are praying for resolution. Sometimes prayers are not enough.

As the conservative MP who speaks for the synod in parliament said: "I think the great danger for the church following the vote is that it will be seen increasingly as just like any other sect." Indeed, this is how many of us already regard it. The question then becomes how can the church continue to function as an arm of the state when it endorses such out-and-out prejudice?

Remember there are already 3,600 women priests in the church and 37 women Anglican bishops worldwide. Africa has just got its first woman bishop. So now we lag behind Swaziland.

The issue is not belief – people can believe in fairies as far as I am concerned – it is the relationship between church and state. In this crazy chess game, the head of the Church of England, the Queen, could not be a bishop. David Cameron has urged them to "get on with it" – ie, vote the right way for the church – but not conforming to equality legislation is untenable.

It is worth understanding what the objection to women as bishops is based on. Evangelicals believe that women cannot exercise authority over men. They use scripture (St Paul's letters) to justify this: "I do not permit a woman to teach or have authority over a man." Thus a man could never swear a canonical oath to a woman bishop. Other objections rest on the fact that Jesus chose only male disciples. Was Jesus sexist? And that before The Fall, when it all went wrong, women existed to act only as helpers to men. I venture that the people, many of them women, who believe such things are unlikely to be swayed by new-fangled notions of equality. But why should they hold such sway in the church and why should the church hold such sway in our land?

Away from theological debate, other issues are at stake. Money, for instance. Reform, the group that represents the evangelicals, holds the rest of the church to ransom by constantly reminding the House of Bishops of its financial clout. In 2010 Reform wrote a letter mentioning the £38m that it had added to the CofE central coffers. The threat that these people withdraw completely from the CofE appears to paralyse the church – but surely the situation has become ridiculous.

The church, in seeking to be above the law, is now a discriminatory organisation, though it holds 26 seats in the House in Lords, from which women are barred. This effective debarring of women from the legislative process is more than an "embarrassment", it is profoundly undemocratic.

A secular country – and that is largely what we are – should have no truck with this. Why on earth should we respect this bizarre sect any longer? The separation of church and state is long overdue. An institution that allows the maintenance of a stained glass ceiling for its female clergy to bang their heads against should not only lose its moral authority. Let it also lose its unearned privileges.