St Paul's Cathedral looks set to reopen tomorrow as The Church of England appeared to be in the grip of a crisis of conscience surrounding its stance on London's anti-capitalist protest. Those camping outside the cathedral, which was shut for the first time since the Blitz last Friday, were campaigning to topple the capitalist system – but yesterday succeeded in creating division within the church.

Last night, as the cathedral remained closed for a fifth day and a legal bid to remove the 200 tents of Occupy London was launched, the Dean of St Paul's, the Right Reverend Graeme Knowles, said he was optimistic the cathedral, which is in the heart of London's financial district, would reopen to the public.

The decision "followed significant changes to the layout of those dwelling in tents outside the Cathedral, " he said.

He added: "We reiterate our basic belief in the right to protest as well as requesting that those people living in the tents now leave the site peacefully."

The statement offered little insight into the church's stance on the protests or hints to the turmoil of the last 48 hours.

St Paul's had been forced to close on Friday because of health and safety issues, the Dean said, though the cathedral refused to make public that advice or say who gave it.

Richard Chartres, the Bishop of London and third most senior cleric in the Church of England, echoed the call, saying the protesters "should leave". But one of the cathedral's chapter members, Canon Giles Fraser, was understood to have threatened to resign if the church tried to rid its grounds of the demonstrators.

His views echoed many of those in the church who felt the demonstration, campaigning against corporate greed and for a better distribution of wealth, seemed a perfect fit with Christian teaching.

Richard Harries, Baron Harries of Pentregarth, the former Bishop of Oxford, who sits in the House of Lords, said the decision to close the cathedral was "sad and mistaken". "Capitalism at the moment is working against the most vulnerable. It is absolutely right the church support those hardest hit by the present economic climate," he said.

"I hope the church stays open for worshippers and tourists who have come from the ends of the earth to get there.

"[But] I do believe the church should support voices who speak for those who are most marginalised. It is not anti-capitalist."

One church insider with knowledge of the debates going on at St Paul's said there was a growing feeling the church was appearing out of touch.

He said: "The church has repeatedly killed off radicalism with a great big hug and depressingly this is yet another example of that. The Archbishop of Canterbury is now in a precarious position because the Bishop of London has well and truly nailed his colours to the mast. If he makes some sort of intervention he will either be seen to be backing the church hierarchy or overriding his own bishop."

Jonathan Bartley, from Christian think-tank Ekklesia, said many middle and lower ranking clergy in the capital were deeply uncomfortable about Bishop Chartres' position. He said. "It's a missed opportunity for the Church to show that it is on the side of the people rather than the current economic system."

The City of London Corporation said yesterday it was considering a High Court bid to remove 200 tents belonging to Occupy London protesters.