Editor's Note: R. Albert Mohler Jr. is president of the Southern Baptist Theological Seminary, the flagship school of the Southern Baptist Convention and one of the largest seminaries in the world.

By R. Albert Mohler Jr., Special to CNN

(CNN)–Cultural upheavals often occur in the most surprising contexts. Who expected that a clash between sexuality and religious liberty would be focused on a restaurant company mainly known for its chicken sandwiches?

And yet the controversy over Chick-fil-A is a clear sign that religious liberty is at risk and that this nation has reached the brink of tyrannical intolerance from at least some of our elected leaders.

The controversy ignited when Chick-fil-A President Dan Cathy, son of the company’s legendary founder, Truett Cathy, told a Baptist newspaper that he and his company “operate on biblical principles” and “are very much supportive of the family — the biblical definition of the family unit.”

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Defining Chick-fil-A as “a family business,” Cathy went on to say that “We intend to stay the course. … We know that it might not be popular with everyone, but thank the Lord, we live in a country where we can share our values and operate on biblical principles.”

Media attention to Cathy’s comments revealed a radio interview he had given a few weeks earlier in which he commented that “I think we are inviting God’s judgment on our nation when we shake our fist at (God) and say, ‘We know better than You what constitutes a marriage.'

“I pray God’s mercy on our generation that has such a prideful, arrogant attitude to think we would have the audacity to redefine what marriage is all about,” he said.

Within days, elected officials in Chicago, Boston and New York were pledging to deny the company access to their cities.

“Because of (Dan Cathy’s) ignorance, I will deny Chick-fil-A a permit to open a restaurant in my ward,” Chicago Alderman Proco Moreno said, in a threat echoed by

Chicago Mayor Rahm Emanuel.

Boston Mayor Thomas Menino was just as blunt: “Chick-fil-A doesn’t belong in Boston,” he said. “We’re an open city. We’re a city at the forefront of inclusion.”

But the kind of inclusion he had in mind would evidently exclude Chick-fil-A.

New York City Council Speaker Christine Quinn, who just recently married her lesbian partner, called upon New York University to kick Chick-fil-A off its campus.

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Echoing the Boston mayor’s lack of irony, she also called for exclusion in the name of inclusion: “We are a city that believes our diversity is our greatest strength, and we will fight anything and anyone that runs counter to that.”

Within days, Moreno, Emanuel and Menino had qualified their statements somewhat, promising to operate within the law and constitutional limits. Those clarifications became necessary when legal authorities quickly recognized threatened violations of First Amendment rights.

To his credit, New York Mayor Michael Bloomberg, an ardent supporter of same-sex marriage, warned, “You can’t have a test for what the owner’s personal views are before you decide to give a permit to do something in the city.”

Note carefully that Chick-fil-A was not charged with discrimination in hiring or service but simply with the fact that its president and chief operating officer supports traditional marriage.

Note something else: Dan Cathy’s statements were explicitly religious. He made his comments to the religious press, including a Baptist newspaper. His comments were infused with his Christian convictions, the same convictions that have led the company to close for business every Sunday.

The threats made against Chick-fil-A betray the principle of religious liberty that is enshrined within the U.S. Constitution. Civic officials in some of the nation’s largest and most powerful cities have openly threatened to oppose Chick-fil-A for the singular reason that its president openly spoke of his Christian convictions concerning marriage.

When Quinn, one of the most powerful officials in New York, announces, “I do not want establishments in my city that hold such discriminatory views,” is she also threatening the Roman Catholic Church, Orthodox Jewish synagogues and Islamic mosques?

They, along with evangelical Christian denominations, openly oppose the legalization of same-sex marriage. Cathy’s statements are completely consistent with his own denomination’s statement of faith and official declarations. He was speaking as a Christian and as a Southern Baptist, and he was speaking as a man who does his best to live and speak as he believes.

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When Emanuel and Moreno tell Chick-fil-A to stay out of Chicago, are they audacious enough to deliver that same message to the churches, mosques and synagogues of their city that also oppose same-sex marriage? What do they do with the fact that their own state does not allow same-sex marriages?

This country is deeply divided over the issue of same-sex marriage, and the controversy over Chick-fil-A is an ominous sign that many of the proponents of same-sex marriage are quite willing to violate religious liberty and to use any and all means to silence and punish any individual or organization that holds the contrary view – a view sustained by the voters in 29 states by constitutional amendments.

Addressing the intersection of same-sex marriage and religious liberty, George Washington University law professor Jonathan Turley has warned that the government must not be “viewed as unfairly trying to pre-determine the debate or harass one side.”

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That is exactly what some elected officials have just shown themselves ready to do. It will not stop with Chick-fil-A. Who will be next to be told to get out of town?

Disclosures:

I know Dan and Truett Cathy and other members of the Cathy family. Truett has spoken on our campus. I have prayed at the opening of multiple Chick-fil-A locations. I serve on the board of directors of Focus on the Family, which has been supported by Chick-fil-A. My son, Christopher, is a part-time service employee of a local Chick-fil-A restaurant in Louisville. I have not communicated with Chick-fil-A about this column.

The opinions expressed in this commentary are solely those of R. Albert Mohler Jr.