The Church of England's General Synod a fortnight ago voted narrowly to permit priests to bless same-sex marriages and kicked off a hell of a storm in the Protestant church in Africa.

In East Africa, an angry Church of Uganda announced that it had started the process of splitting from Canterbury, the seat of the Anglican Church.

The Anglican Church of Kenya also pronounced its displeasure and suggested it, too, might seek separation from the mother church.

Many probably missed the fact that the Church of England's decision, while a major shift, was not particularly radical. Same-sex couples still can't be wedded in the church. They will only get a nod and wink from a priest after they have had their civil wedding elsewhere.

The vitriolic response of the Anglican churches in East Africa couldn't be more ironic. First, the church was never really theirs. It has its roots in the immediate pre-colonial and colonial period, brought to these shores by the British.

Property

Like in divorce, it will be interesting to see what happens to the property. Do they walk away with the flock or take the buildings too? This is because most of the establishment Protestant (and Catholic) churches are still sitting in houses of worship built by mzungu missionaries before independence.

However, most surprising is that the African chapters of the Church of England think that the worst sin ever committed by the church is blessing gay marriages.

About three weeks before the General Synod vote, the Church of England said it felt "real shame" after admitting it knew it was investing in the trans-Atlantic slave trade during the 18th century following a report that it commissioned last year. It committed $121 million to redress the wrongs of links to the slave trade.

The Church Commissioners, who manage the church's £10 billion ($12 billion) investment portfolio, will use the money for a fund that it will invest in communities affected by past slavery and conduct research and engagement related to the church's ties to slavery.

Slave-trading company

The predecessor of the investment fund, the Queen Anne's Bounty, invested significant amounts in the slave-trading South Sea Company in the 18th century.

Following the report, there was no threat of cutting ties with the Church of England. One would have thought that the brutal slave trade, in which more than 15 million Africans were victims and nearly two million died as Europeans were transporting them to the Americas, would be a greater moral sin. But no, a decision to bless marriages of people who love each other, but are gay, is the red line.

Nevertheless, this upheaval could result in a dramatic political change in the countries where the Anglican Church comprises the majority religion. And it has to do with money. The old Christian churches are struggling to keep the lights on, their share of wallet eaten away by the numerous independent churches with their miracle-peddling and colourful, artful pastors.

Corruption and incompetence

Money from the Church of England, and its related infrastructure, is important for them. Without it, they will be forced to close shop or function in penury. To compound matters, many leaders of the established churches (Protestant and Catholic) haven't been great visionaries. One reason they haven't built as many churches as the missionaries did before independence is corruption and incompetence. There have been many church-building projects, but the priests and bishops are just like many of our leaders — they have eaten the money.

For the churches to survive, they will have to embrace fully the process that is already underway; they will have to become closely aligned with governments or, at worst, become state departments that get their upkeep directly from national budgets.

As it is, there are already many priests and bishops for rent by politicians.

Cut off from the patronage of the Church of England, it won't be long before they become fused in politics as state religions. While there are countries in Africa where Islam is the state religion, there is none in which a particular Christian church is an official religion, even in countries led by prayerful presidents or those like Malawi or Seychelles, which a former pastor and former priest, respectively, govern.

The while violating it in practice, with presidents stacking the governments they lead with people from their churches.

Overwhelmingly Muslim

In Sudan or Egypt, which are overwhelmingly Muslim countries, the religion of who the next president is doesn't matter. He will be a Muslim.

In Christian countries, it is tricky. Today's president might be Catholic, but tomorrow's Protestant and the chap who leads a coup might be Seventh Day Adventist or a senior member of the Temple of the Lord Who Rules The Mountains and Seas.

The state religion is likely to be ephemeral. For five years, it would be Protestant. At the next election, if a Muslim or Catholic wins, it would be suspended. The religious stakes will get higher, and elections will become more fraught with the risk of violence and state breakdown than they are today. And even where stability is maintained, there could be a sharp pivot toward more socially conservative state policy.

The ban on sex education in schools, which has just happened in Tanzania, would become the order of the day and more extreme. All this because of the homophobia of some of our bishops.

Charles Onyango-Obbo is a journalist, writer, and curator of the "Wall of Great Africans". Twitter@cobbo3