The Church of England took a step towards averting schism over gays yesterday when the General Synod backed a process that would allow the expulsion of rebel provinces from the Anglican Communion.

Some liberals in the established Church oppose the introduction of an Anglican “covenant” outlining a common doctrine that is to be endorsed across all 38 provinces worldwide, because they fear it will limit the traditional diversity that has become a hall-mark of Anglicanism.

But the Synod, meeting in York, voted overwhelmingly to “engage positively” in the creation of the covenant after a series of speakers warned that the dispute over homosexuality had exposed deep flaws in how Anglican unity is maintained. The covenant would prevent any province from consecrating an openly gay bishop, as the US did in 2003 with the election of Gene Robinson to New Hampshire, without risking expulsion.

But the Synod also heard that it would put in place a curial-type structure that would mean other doctrinal innovations would also be jeopardised. One speaker warned that the ordination of women would never have got through had such a covenant already been endorsed.

The Archbishop of the West Indies, the Most Rev Drexel Gomez, who chaired the group that published the proposed draft covenant this year, warned that the “bonds of affection” that once held the Anglican Communion together were strained, “indeed, some would say broken”.

He said: “Suspicion is rife, as well as accusations of heresy, bad faith, and of theological and ecclesiological innovation.”

Rumours abounded that there were plots in some provinces to introduce a bold agenda on gay marriage and to demand that it was tolerated across the Communion, he said. “Other rumours inform us that the primates are plotting to impose a collective papacy on the Anglican Communion.”

He said that those responsible for drafting the covenant would take into account concerns, especially about giving too much power to the 39 Primates to discipline provinces “who choose not to fulfil the substance of the covenant”. But he said there had to be mutual accountability.

“The need for such a common basis is pressing. I have no doubt that it would be lovely to go back to a day when we relied on no more than the affection generated by our mutual inheritance and care. But I’m afraid that those days have gone: at present, Anglican leaders are seriously wondering whether they can recognise in each other the faithfulness to Christ that is the cornerstone of our common life and cooperation.”

Archbishop Gomez’s voice is particularly influential because his province is part of the Global South group of conservative evangelical Churches, although it is actually within the tradition of Anglo-Catholicism.

The Bishop of Chichester, the Right Rev John Hind, said that to reject the creation of a covenant would be “to vote for a different kind of communion”. He said: “An appropriately considered and drawn covenant might help us to love one another more.”

But the Rev Miranda Thelfall-Holmes, an historian representing Durham and Newcastle universities on the Synod, said: “I do not believe signing up to an Anglican covenant will help, either in our current dfficulties or in any other disagreements.”

As the debate opened, so did the heavens, with a thunderstorm. Drops of rain leaked into the debating chamber at York University. Some in the chamber wondered whether this was another “York Minster” moment. York Minster was struck by lightning soon after the then Bishop of Durham, Dr David Jenkins, was consecrated there – an event interpreted as divine retribution for his description of resurrection as “not just a conjuring trick with bones”.