Thorburn announced he would step down from the position yesterday, barely 24 hours after his appointment, following criticism about his role as chairman of City on a Hill.
The church has denounced homosexuality and likened abortions to the operation of concentration camps - a position the Victorian Premier, an Essendon member, said has no place in the sporting community.
Andrew Thorburn has quit his role as Essendon CEO barely 24 hours after his initial appointment.(Essendon Football Club)
"Aren't we all God's children? Like seriously, there is no place for bigotry, there's no place for stigmatising people," Andrews said.
"When it comes to rampant homophobia, when I lead the pride march every year, I do that with a sense of genuine concern, support and commitment.
"If I'm to be criticised for that, so be it."
Essendon president David Barham said Thorburn was given the option between retaining his position with the AFL club or the church, and he chose the church.
Yesterday, Andrews described the position as "absolutely appalling".
"Those sort of attitudes are simply wrong and to dress that up as anything other than bigotry is just obviously false."
City of Port Melbourne Deputy Mayor Tim Baxter said he had resigned his membership and the membership of his children over the decision to appoint Thorburn.
AFL great Matthew Lloyd joined criticism of Thorburn's appointment by the club.
"Wouldn't the club have known earlier that this was going to come back to them?" he said.
"I'm sort of gobsmacked to be honest, that we sit here and it's embarrassing."
Victorian Premier Daniel Andrews said the controversial opinions of the church didn't have a place in the sporting community.(Nine)
Thorburn said yesterday he was "saddened" by the turn of events.
"Yesterday was one of the proudest days of my life," he wrote.
"However, today it became clear to me that my personal Christian faith is not tolerated or permitted in the public square.
"This grieves me greatly."
Catholic Archbishop of Melbourne Peter Comensoli said today Thorburn's religious beliefs should not have cost him his job.
"If the Essendon situation is a litmus test of the value and place of people of faith in Victorian society, then we are in big trouble," he said.
It is outrageous that a person of good character has felt that he must choose between a public leadership role and being an active member of a Christian community.
"Sadly, this situation sends a chilling message to ordinary faith believers in Victoria, that they can't be trusted to exercise leadership and service in the community."
