If you think the A&E Network’s decision to indefinitely suspend the star of its cash cow “Duck Dynasty” made bad business sense, wait until you hear what Cracker Barrel did. Yesterday the restaurant chain that made its name and fortune on the appetites of Southern folk like Phil Robertson and the rest of his duck-calling entrepreneurial family decided to pull some “Duck Dynasty” merchandise from its stores.

In a statement on its Facebook page, Cracker Barrel cited its “pleasing people” motto and its commitment to “the ideals of fairness, mutual respect and equal treatment of all people.” The company then explained why “Duck Dynasty” no longer may reflect those ideals:

We continue to offer Duck Commander products in our stores. We removed selected products which we were concerned might offend some of our guests while we evaluate the situation. We continually evaluate the products we offer and will continue to do so.

It didn’t take long for “Duck Dynasty” fans to voice their outrage to Cracker Barrel, which has more than 67,000 employees at its 600-plus stores. At last check, the Facebook statement had sparked more than 27,000 comments, most of them from regular diners who said they won’t be any longer. The post also has been shared more than 4,900 times, presumably by those same former customers telling their friends to boycott Cracker Barrel in the future.

All of which made me wonder: Why would Cracker Barrel take this stand? The executives and corporate board members who run the chain surely know that most of the people who shop and eat at an “old country store and restaurant” are the enlightened rednecks who sided with the Robertsons. Yet Cracker Barrel decided to cast its lot with A&E, the Gay and Lesbian Alliance Against Defamation, and the Human Rights Campaign.

I found the answer in Cracker Barrel’s corporate history — not the filtered, flattering version the company tells but the version you can find via Google. The key finding: Cracker Barrel has been in trouble with homosexual rights activists before.

How much trouble? Enough that The New York Times emphasized the controversy in its 2012 obituary for Cracker Barrel founder Dan Evins. The paper mentioned the issue in the headline and lead, and expounded on it at length in its coverage:

His tone was considerably harsher when it came to defending a January 1991 directive to all the company’s restaurants to fire employees “whose sexual preferences fail to demonstrate normal heterosexual values.” Mr. Evins’s explanation for the edict was that gay people made customers in rural areas uncomfortable. As many as 16 openly or suspected gay employees were promptly fired.

Protests erupted at restaurants in dozens of cities and towns; boycotts were organized; and shareholders complained. At a time when discrimination against gay people was not prohibited under the laws of most states or the federal government, and many companies practiced it, Cracker Barrel’s action stood out for its sheer blatancy.

“They actually put a policy like this in writing, which was, and still is, shocking,” David Smith, a spokesman for the Human Rights Campaign, a gay rights organization based in Washington, told The Herald-Tribune.

The New York City Employees Retirement System, which owned more than $6 million of Cracker Barrel shares, led other stock owners in using their votes and other legal means to organize resistance.

In March 1991, Mr. Evins apologized and said the policy had been rescinded. But New York and its allies fought until 58 percent of the shareholders in 2002 persuaded Cracker Barrel’s board to vote unanimously to explicitly forbid anti-gay discrimination in its equal employment policy.

Cracker Barrel still didn’t have any respect in the homosexual community in 2002 when the Human Rights Campaign debuted its corporate equality index, which rates companies based on how they treat homosexual, bisexual and transgender employees. It was one of three companies to score a zero in the index.

The company boosted its score to 29 a year later “by withdrawing its opposition to a shareholder proposal asking the company to include sexual orientation in its non-discrimination policy and subsequently adopting such a policy.” Cracker Barrel’s ratings have fluctuated between 15 and 55 since then, but the Human Rights Campaign has periodically praised the company for strides on the gay rights front.

In 2011, for instance, the group noted that Cracker Barrel had moved well beyond its much-derided pink-slips-for-gays policy. By then the company had included sexual orientation in diversity training and had even made a cash grant to the Tennessee Equality Project.

More to the point, Cracker Barrel earned kudos when the Human Rights Campaign released its 2014 ratings just days before the “Duck Dynasty” controversy. The Huffington Post cited Cracker Barrel’s progress on gay rights in a story headlined “HRC’s Corporate Equality Index Shows Southern Companies Evolving on Gay Rights.”

In the early ’90s, Southern restaurant chain Cracker Barrel drew criticism from gay rights activists for firing openly gay employees under a policy that required workers to display “normal heterosexual values which have been the foundation of families in our society.”

The company’s policies largely reflected the times. Sodomy was still a crime, and it was legal in many parts of the country — and continues to be today — to fire someone based on their sexual orientation. But experts say that Cracker Barrel’s stance has evolved, a sign that the movement’s victories go beyond the big cities of the coasts and the Midwest.

In an annual survey assessing corporate practices relevant to LGBT employees published this week by Human Rights Campaign, Cracker Barrel was given a score of 45 out of 100, a 10-point boost from the previous year. …

“Our mission is about pleasing people,” Terry Deas, Cracker Barrel’s director of diversity and outreach told The Huffington Post. In 2013, the company focused on adding LGBT content to its employee training seminars, participating in local LGBT educational events, and trying to recruit more LGBT employees and partner with LGBT-owned companies. “It was all about living the mission of our company.”

With good press like that, it’s no surprise that Cracker Barrel chose to pull Duck Commander merchandise from its shelves. Leaving it there could have alienated a gay rights group that had just made it look good and that had slammed Robertson, the 67-year-old Duck Commander patriarch.

Cracker Barrel may have another reason to distance itself from Robertson. In the same GQ interview where he coarsely stated his views on homosexuality, Robertson discussed his experience with blacks as a poor white man in the 1960s South. Some critics have characterized his comments as racist, and Cracker Barrel had a race controversy of its own a decade ago.

The Justice Department investigated claims of racial discrimination against black diners in about 50 restaurants across seven Southern states. Cracker Barrel settled with the federal government in 2004 by agreeing to various conditions. That same year, Cracker Barrel agreed to pay $8.7 million to settle lawsuits brought by at least 42 plaintiffs.

A two-decade string of controversy involving discrimination over sexual orientation and race has a way of shaping a public corporation’s approach to potentially explosive partnerships. It clearly convinced Cracker Barrel’s head honchos that the Robertson family is just too toxic to embrace unconditionally.

But that decision appears to be backfiring for now. Chick-fil-A may get a whole lot more business from enlightened rednecks who are angry at Cracker Barrel. As one consumer said on Facebook: “After you are done removing the selected products, go ahead and remove a bunch of tables and chairs. You won’t be needing them any more.”