As far as conservative organizations are concerned, being labeled a “hate group” by the Southern Poverty Law Center isn’t just annoying — it’s dangerous.

Gunmen have twice targeted conservatives specifically cited by the SPLC for hate: Republican Rep. Steve Scalise, who was shot June 14 by a fan of the SPLC Facebook page, and the Family Research Council, whose security guard was wounded in 2012 by a man who said he found the FRC on the SPLC’s list of “anti-gay groups.”

So when GuideStar USA, a self-described “neutral” database of nonprofits, decided this year to slap the SPLC’s “hate group” tag on 46 groups, including the FRC, conservatives declared enough.

“Southern Poverty Law is an arm of the left,” said Jerry Boykin, FRC executive vice president, who joined 40 other conservative leaders in a June 21 letter to GuideStar. “To use their data is just incredible, particularly when the results can be exactly what we experienced at Family Research Council when we had a shooter.”

After initially standing by the SPLC tags, GuideStar CEO Jacob Harold agreed Tuesday to remove the designations, citing a commitment to objectivity as well as “concerns for our staff’s well-being.”

He said some employees had faced harassment.

At the same time, he said the charity tracker would continue to provide SPLC data to interested parties.

“We will continue to make this information available upon request to anyone who seeks it,” Mr. Harold said. “And we are actively exploring how else we might be able to share information on those groups that abuse nonprofit status to advance an agenda of hate.”

That wasn’t enough for the Liberty Counsel Chairman Mat Staver, who announced Wednesday that the group had filed a lawsuit against GuideStar for what he described as its “reckless defamatory and harmful political labeling.”

“The only purpose of providing the SPLC false and dangerous ‘hate group’ label is to inflict reputational and financial harm to Liberty Counsel,” Mr. Staver said. “GuideStar has lost all credibility.”

The SPLC rushed to GuideStar’s defense, saying, “We stand ready to support our designation of Liberty Counsel as a hate group.”

“Liberty Counsel is a group that has consistently called LGBT people ‘immoral, unnatural and self-destructive,’” said SPLC President Richard Cohen. “It has a track record of attempting to criminalize homosexual conduct and to legalize discrimination against the LGBT community.”

With more than 2 million profiles, GuideStar has billed itself as the “world’s largest nonprofit database,” but conservatives said the episode has raised troubling questions about whether the charity tracker harbors a political agenda.

Philanthropy Roundtable’s Karl Zinsmeister, a former adviser to President George W. Bush, took the SPLC to task this year, calling its extremist list a political tool, not a “Consumer Reports guide,” and describing the organization as a “cash-collecting machine.”

Mr. Harold acknowledged that the SPLC has been accused of political bias and being “too focused on fundraising,” but he concluded that “no data source is perfect.”

He said GuideStar’s concern lies with combating those who “abuse nonprofit status to spread hateful rhetoric.” He defined hate as the attempt to “denigrate or marginalize a group of people based solely on their identity.”

“We have seen overwhelming evidence that hateful agendas have been pushed by individuals within nonprofit organizations,” Mr. Harold said. “There can and must be a debate regarding how we define ‘hate,’ but we do believe it is within GuideStar’s mission to help the public understand how its philanthropic dollars are used.”

The right has long decried the SPLC’s “guilt by association” approach, in which major conservative organizations such as FRC are listed as “hate groups” alongside extremist outfits like the Ku Klux Klan and Westboro Baptist Church.

The groups flagged by GuideStar included white supremacist Richard Spencer’s National Policy Institute as well as leading conservative nonprofits like the Alliance Defending Freedom, Eagle Forum and Federation for American Immigration Reform.

Among those signing the letter urging GuideStar to stop using the SPLC labels was former Reagan Attorney General Edwin Meese.

The SPLC was hardly discouraged by GuideStar’s decision to take down the tags.

“We appreciate that GuideStar will continue to provide information as to whether the organizations they rank are designated as hate groups by the Southern Poverty Law Center,” the center said in a statement.

“At a time when hate groups increasingly present a mainstream veneer, the public deserves such information,” said the SPLC. “We respect that GuideStar is reassessing how to make that information available.”

Mr. Cohen had previously condemned as “sickening and cowardly” the attack on Mr. Scalise, during which the gunman, 66-year-old James Hodgkinson of Illinois, also struck a congressional staffer, a lobbyist and two Capitol Police officers.

“We’re aware that the SPLC was among hundreds of groups that the man identified as the shooter ‘liked’ on Facebook,” Mr. Cohen said in his June 14 statement. “I want to be as clear as I can possibly be: The SPLC condemns all forms of violence.”

Mr. Harold described GuideStar as nonpartisan, but critics have questioned his political leanings. He was previously affiliated with the Rainforest Action Network and Greenpeace USA, and donated to President Obama’s campaign in 2011 before starting at GuideStar in 2012.

Mr. Harold posted a photo of himself on Twitter at the Jan. 21 Women’s March holding a sign that said, “It turns out that facts matter.”

“Which is perfectly OK as long as you don’t portray your organization as a neutral organization,” Mr. Boykin said, “and that’s what he’s trying to do.”

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