I realised that beards and soft words do not a liberal make when the Archbishop of Canterbury toured the Sudan in 2006. His visit coincided with the first genocide of the 21st century: the massacres in Darfur. The forces of the Arab-supremacist government in Khartoum were fighting a war to the knife with black Africans that left hundreds of thousands dead. The slaughter might not have been happening as far as Rowan Williams was concerned. He was the regime's guest and refused to bear witness to the suffering or criticise its perpetrators.

I thought at the time that among the reasons why I could not believe in God was the shabbiness of his representatives on Earth. The archbishop's officials explained that he did not wish to be undiplomatic, but I did not wholly believe them either. Williams seemed just the type to believe that crimes against humanity were colour-coded. One should denounce atrocities committed by the west, of course, but stay silent when the criminals had black or brown skins for fear of being thought a cultural imperialist or neocolonialist.

Now that Williams and his fellow bishops are so angry at the possibility of civil gay marriage they are talking of disestablishing the church, we should acknowledge that Williams has always been prepared to accommodate reactionary forces abroad to further reactionary ends at home.

Those who knew him when he was young are shocked. He was once liberal on the question of whether Anglicans should tolerate gay and lesbian love and openly homosexual priests. As the church has had closet cases for two millenniums, who have lied to themselves, their congregations and, on occasion, to the poor women they manoeuvred into loveless marriages, I would have thought that honesty would have been the best argument for equality. But as we have seen, honesty is not a virtue the archbishop treasures.

Instead, Williams developed an eccentric but, I happily admit, touching line of thought. He took a scene in Paul Scott's Raj Quartet in which Sarah Layton, a respectable daughter of the regiment, is seduced by a worthless man. Williams told members of the Lesbian and Gay Christian Movement in 1989: "There may be little love, even little generosity, in Clark's bedding of Sarah, but Sarah has discovered that her body can be the cause of happiness to her and to another. It is this discovery which most clearly shows why we might want to talk about grace here. Grace, for the Christian believer, is a transformation that depends in large part on knowing yourself to be seen in a certain way: as significant, as wanted."

Like Sarah Layton, gays and lesbians also deserved the body's grace. Even in the Bible, "there is a good deal to steer us away from assuming that reproductive sex is a norm". His words read as well today as they did then, but Williams has forgotten what he once knew.

His conversion came when traditionalists rounded on him for allowing Dr Jeffrey John, a gay dean in a celibate relationship with another priest, to become Bishop of Reading. Conservative Anglicans turned to the poor world to find believers who could make Williams back down. Giles Fraser, who bravely in my view resigned from St Paul's because he could not accept the church's decision to clear the Occupy protesters camping by the cathedral, told me he has never forgotten the hypocrisy of the moment. In 2003, religious conservatives who had never been out of Britain flew to Africa to recruit reserve armies of reactionaries from the Anglican communion. "Until then we had rarely thought about the Anglican communion," Fraser said. "There was just a collection box at the back of the church for Christians abroad." He soon realised that a new force had arrived in church politics. From then on, the Church of England could not settle its own affairs according to its conscience. It had to consult an "Anglican communion" that tolerated the unconscionable.

The African bishops played on Williams's white man's guilt. Decent treatment for homosexuals was an imperialist assertion of western values, they implied. Williams folded and forced John, who was once his friend, to stand down. He admitted that among his motives was his desire to appease the "resentment toward the United States and England in some former colonial areas".

The fault of anti-imperialist politics in either its left or liberal forms is its inability to see distinctions among the formerly colonised. Williams's retreat has mollified the Ugandan Archbishop Henry Luke Orombi, who says: "Homosexuality is evil, abnormal and unnatural as per the Bible." Williams has kept him on board. Held the Anglican communion together.

But how can Anglicans oppose the Ugandan government's attempts to mandate death sentences or life sentences for homosexuals? Can Anglicans expect anyone to believe them when they say there is no connection between theological justifications for homophobia and the terror the Ugandan state and the Ugandan Anglican church wish to direct against homosexuals?

The language of "communion" and "engagement" sounds kind and woozy. There is nothing kind about the prison cells that await gay men in Kampala – nor grace behind their bars.

As with gays, so with women. Anglicans in 42 of the 44 dioceses of the Church of England say they want women bishops. They have offered the services of outside male bishops to the minority of parishes who cannot accept a woman in authority. The generous concession was not enough. So Williams cut a deal with the misogynists. He proposes that not only can they have male bishops, but male bishops who have not been ordained by a woman, or ordained a woman themselves or even taken communion from a woman. (Williams will have to appoint bishops who were born to a sinful woman, but one suspects that if he could find men without mothers he would take them.)

The church's complaint that civil gay marriage may, despite the government's assurances to the contrary, lead to the European Court of Human Rights forcing it to marry homosexuals at some unspecified point struck me as fanciful and neurotic. But when church sources tried to scare the government into submission by raising the prospect of disestablishment, they spoke truer than they knew. England accepts the emancipation of women. England is on it way to accepting the emancipation of homosexuals. The Church of England cannot stand against the settled will of England and expect to remain the national church.