Members of synagogues involved in the social action group London Citizens hit back at JC criticism in a session entitled "Is the JC waging jihad on the Jews who engage?"
Matt Plen, director of the Assembly of Masorti Synagogues and a trustee of London Citizens, said that the depth of opposition had taken him by surprise.
Controversy has flared up because one of the founding organisations of London Citizens is the East London Mosque, which critics say has played a prominent role in the promotion of political Islamism.
But most of those who spoke among the 60-plus audience defended the continuing involvement of members of New North London and Finchley Reform synagogues in the coalition.
Keith Kahn-Harris, co-author of a book on modern British Jewry, Turbulent Times, sharply attacking the JC's editorial stance, contrasted "the politics of engagement" with the "'Judaean People's Front' politics of exclusion".
Barend Velleman, an NNLS member involved in London Citizens' North London branch, said that if young Jews and Muslims did not start engaging with each other, "the next generation will be at war with each other".
His son Liron, chairman of the NNLS youth council and a JFS sixth-former, said he had asked his school to consider joining London Citizens.
But Adrian Cohen, chairman of the London Jewish Forum, argued that while he did not subscribe to a "policy of isolation", giving legitimacy to hardline Muslim groups risked undermining liberal Muslims.
He defended the record of JC political editor, Martin Bright, who, said Mr Cohen, had stood unflinchingly against fanaticism and antisemitism.
At another session on British Muslims, Mohammed Aziz, a trustee of the East London Mosque, said it was important to realise the diversity within the mosque which had a footfall of up to a quarter-of-a-million people each month. "It is very diverse ethnically, but also in terms of denominations, beliefs and practices," he said.
"There are bound to be many views which you will find unacceptable… there are many I would find unacceptable."
He cited the mosque's recent grant to the neighbouring Fieldgate Street Synagogue to repair its roof as one positive instance of Muslim-Jewish relations. "There are some really good examples of what the moderates within that mix of the congregation have been able to achieve," he said.
But Mr Aziz said the mosque often gets "a very bad press… That makes our life more difficult when the moderates are lumped in with the extremists."