Religious organizations that discriminate against the LGBT community have been stunned by the US supreme court’s ruling handed down last week that it is against the law for employers to fire LGT employees because of their sexual orientation or identity.

The ruling would have “seismic implications” for religious freedom and would potentially set off years of lawsuits for religious organizations, said Russell Moore, the president of the public policy arm of the Southern Baptist Convention.
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“I am deeply concerned that the U.S. Supreme Court has effectively redefined the legal meaning of ‘sex’ in our nation’s civil rights law,” the president of the Catholic bishops’ conference, Archbishop José H. Gomez, said in a statement. “This is an injustice that will have implications in many areas of life.”
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But what conservative religious groups may see as a religious freedom issue, secular and progressive religious groups see as an excuse to discriminate.

The question is whether there will be an exemption carved out for religious organizations like the Catholic or evangelical churches, allowing hem to fire (or not hire) any employees just because they are LGBT. We are now going to see those groups try use the Religious Freedom Restoration Act (RFRA) to argue that they are not bound by the latest ruling, something that justice Gorsuch anticipated in his majority opinion ruling, but he said that those issues were not before the court in this case and will have to await a future case.

In his opinion, Justice Gorsuch recognized the existence of several religious freedom protections, including the First Amendment, the Religious Freedom Restoration Act of 1993 and a 2012 Supreme Court ruling that recognized a “ministerial exception” in employment discrimination laws.

But he signaled that Monday’s decision could lead to a fight over the validity over those protections. “How these doctrines protecting religious liberty interact with Title VII are questions for future cases too,” he wrote.
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Forecasting a coming fight over religious liberty, Americans United for Separation of Church and State urged a unified strategy. “The progressive, inclusive faith and secular communities must come together to make clear that religious freedom is a shield that protects, not a sword that licenses discrimination,” the group’s president, Rachel Laser, said in a statement.

We will very likely see a court challenge in the near future when a religious organization fires an employee whom they discover is LGBT and then claims that RFRA grants an exemption from this ruling.