Francis Cardinal George says city officials like the mayor should not be in charge of deciding the values of Chicagoans.
Emanuel, who said he has chosen not to escalate the debate, believes that "enough has been said already."
"I'm here for the kids. I expressed my view in support of gay marriage and legalizing civil unions. Are you defining Chicagoans? No, I am expressing them," said Emanuel.
On Wednesday, thousands of Chick-fil-A customers recognized "Chick-fil-A Appreciation Day." A record number of customers ate at more than 1,600 Chick-fil-A locations across the nation. Friday's "Kiss In" was planned in response.
"I think it's blown out of proportion. It's sad that we have to go to both extremes of this," said Stephanie Brenneman.
Emanuel is not the only city official expressing his views on the topic.
Chicago Alderman Joe Moreno has said he would oppose Chick-fil-A's plan to expand in Chicago.
The mayor of Boston told the chain, "I urge you to back out of your plans to locate in Boston."
The mayor of San Francisco, where the closest Chick-fil-A is 40 miles away, said, "I strongly recommend that they not try to come any closer."
Harold Krent, dean of the Illinois Institute of Technology's Kent College of Law, says the government cannot stop business from expanding based on an owner's opposition to gay marriage.
"This is where a fine line is drawn, and you have to make clear that official decisions, permitting, licensing aren't based on religious beliefs or political ideology," said Krent.
Krent added that when elected officials express their opposition based on differing values, it draws more public scrutiny to zoning, permitting and licensing.