The decision by St Paul's Cathedral to drive protesters from its steps using force threatens to further divide the Church of England.

The hundreds of protesters camped on church land, who want to draw attention to the role the City has played in the financial crisis, as well as its continued high pay and bonuses.  The Archbishop of Canterbury, Dr Rowan Williams, privately despairs of the cathedral's handling of the financial protest, The Independent understands.

Dr Williams's natural sympathies lie with the protesters but because of Church of England politics he does not want to be seen to interfere. His silence, and that of high-ranking bishops, has left the Church's leadership accused of not practising what Jesus preached – caution against greed and furtherance of a distribution of wealth.

The decision to seek a legal injunction against the protesters yesterday immediately prompted the resignation of a junior chaplain, the Rev Fraser Dyer. Compared with Giles Fraser, the former Canon Chancellor of St Paul's who resigned on Thursday, Mr Dyer is a minor figure, but his departure will cause consternation among the lower ranking clergy at St Paul's, some of whom are less than happy with the route their leadership is pursuing.

Mr Dyer's resignation letter articulated the crux of the problem. "I appreciate that St Paul's has its own means of speaking to the issue of corporate and financial conduct in the City," he said, "but am sorry that a way could not be found of – at the very least – continuing to [support] the occupation of the precinct by those with a genuine and prophetic complaint that has much in keeping with the values of the gospel."