People on both sides say it's an equality and freedom issue. On one hand, the freedom to marry whom you choose and on the other hand, freedom to do business regardless of your beliefs.
Armitage Baptist Church Pastor Charles Lyons read a letter addressed to the mayor on Sunday.
"Mr. Mayor, please do not dismiss us. Do not disrespect us," the letter read.
It comes five days after the mayor entered the Chick-Fil-A fray, with comments condemning the anti-gay marriage position of the restaurant's president.
"Chick-Fil-A's values are not Chicago values," Emanuel said on Wednesday.
"We love our city," Lyons said. "We love our neighbors with whom we may disagree. We too are Chicago!"
Armitage Baptist is in the Logan Square neighborhood where plans to building a new Chick-Fil-A are now up in the air after Alderman Joe Moreno said he opposed its construction.
"When we look at zoning, when we look at having businesses in our ward, we have to look at the responsible actors," Moreno said on Wednesday.
The issue has sparked nationwide protests.
"You're making this about something it isn't. This is America!"
And Sunday morning, it was the talk of the weekly political shows.
"The head of Chick-Fil-A is being excoriated by these people, by Rahm Emanuel for example," said ABC News political contributor George Will. "The gay rights movement isn't driving this. The gay rights movement is far too sensible. These are pandering, third-rate politicians pandering to them."
But Chick-Fil-A's critics say its president's opposition to gay marriage goes beyond words.
2010 tax documents show Chick-Fil-A's charitable arm gave nearly $1.2 million to the Marriage and Family Foundation, an Atlanta-based non-profit whose chairman is Donald Cathy, a Chick-Fil-A vice president and son of the company's founder.
The group's mission statement to the IRS: "...to effect cultural change" in the gay marriage debate through "a public awareness message and campaign."
Celebrity chef Art Smith was serving up his own chicken at a fundraiser for the group Equality Illinois, which is calling for a Chick-Fil-A boycott.
"We say a big thank you to the mayor and a big thank you to the alderman," Smith said. "It is not Chicago values. This city is made up of people from all over the world."
Smith married his husband, Jesus Salguiro, in Washington, DC two years ago.
"Basically what they're preaching is hate, and we will not tolerate that in this city," said Salguiro. "We don't want it, and take it somewhere else."
The Chicago Republican Party says it plans to take action in defense of the planned Logan Square Chick-Fil-A.
The party says that on Wednesday it will file anti-discrimination complaints with the Illinois Department of Human Rights and Attorney General's office.