Islamic State claimed responsibility for the murder of Fr Jacques Hamel, as well as the attack in Nice earlier this month where 84 people were killed by a man who drove his lorry down a seaside promenade on Bastille Day.
The head of the main Muslim umbrella group Anouar Kbibech, who attended Friday's gathering, reiterated a call for Muslims to visit churches on Sunday to show solidarity with Christians as they pray.
Another imam directly attacked the killers who claimed to act in the name of Allah.
"You have the wrong civilisation because you are not a part of civilisation. You have the wrong humanity because you are not a part of humanity," said Abdelatif Hmitou.
"You have the wrong idea about us (Muslims) and we won't forgive you for this.
"How may the idea reach your mind that we might loathe those who helped us... to pray to Allah in this town? How could you think that, Mister killer? Mister criminal?"
He was referring to the help by the St Therese church adjacent to the mosque that sold the plot of land to the Muslims for a symbolic sum so they could build a house of worship.
The two 19-year-old attackers who murdered Fr Hamel were killed by police as they left the church, where they had held two nuns and an elderly couple hostage as they slit the priest's throat.
Three people were being held on Friday for questioning in the attack, including a Syrian refugee, a judicial official said.
The Reverend Pierre Belhache, in charge of relations with the Muslim community, said: "We won't let anyone divide us.
"It is so rich to have these differences but still be together."
