A banner held by two supporters as Ms Walker spoke read: "Antisemitism is a crime, Anti-Zionism is a duty."
Rt Rev Dr John Armes later issued a statement explaining his decision, saying: "We support freedom of speech; we also seek close and friendly relationships with people of every faith.
"On this occasion I considered that these two important values collided. I believe that the organisers of all political gatherings must take care to ensure that individuals and religious groups are not singled out for abuse because of their beliefs.
"My advice was that it would have been unacceptable for a gathering to take place in one of our churches that might encourage such abuse."
An email explaining the ban was also sent to the rector of St Columba's Scottish Episcopal Church, David Paton-Williams.
The rector said: “Criticism of Israel’s policies can have unintended consequences, leading to an increase in antisemitic attacks."
He added: "I have been in consultation with the bishop, to gauge the wider implications of the event, and to ask his advice.
"Having talked it over with him, I am writing to let you know that St Columba's is cancelling the booking for Monday night's meeting. I do not do this lightly and I regret that it is at this short notice."
