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Sister Caroline attends a 2014 rally in Chicago with other supporters of religious freedom to praise the Supreme Court's decision in the Hobby Lobby contraception coverage requirement case. | Getty Court: Hobby Lobby ruling OKs some employment discrimination

A Supreme Court decision allowing some companies to opt out of portions of Obamacare for religious reasons also guarantees the right of firms to engage in religiously motivated discrimination against their employees on the basis of gender, a federal judge in Michigan ruled Thursday.

U.S. District Court Judge Sean Cox held that the Supreme Court's 2014 ruling on a suit brought by Hobby Lobby craft stores means the Detroit-based RG & GR Funeral Homes was legally protected when the firm fired Aimee Stephens, a transgender employee who wished to dress as a woman.

While the ruling involved a dispute over a transgender employee, the logic could apply to any type of gender or race discrimination a company says is motivated by religious views, lawyers tracking the case said.

Cox said the 1993 Religious Freedom Restoration Act, as interpreted by the justices in Hobby Lobby, meant that the sincere religious beliefs of closely held companies like RG & GR had to be respected unless the government could show a need to advance a compelling interest and that letting Stephens wear women's attire would have the least impact on the religious views of the company's management.

"Thus, the question becomes whether the law at issue here, Title VII and the body of sex-stereotyping case law that has developed under it, imposes a substantial burden on the ability of the Funeral Home to conduct business in accordance with its religious beliefs," the judge wrote. "The Court concludes that the Funeral Home has shown that it does."

Cox noted a statement on the funeral home's website that said the company's "highest priority is to honor God in all that we do as a company and as individuals" and that one of the owners believes that the "Bible teaches that a person’s sex (whether male or female) is an immutable God-given gift and that it is wrong for a person to deny his or her God-given sex.”

The suit was brought by the Equal Employment Opportunity Commission, which Cox faulted for failing to try to reach an accommodation with the funeral home. The judge said the EEOC demanded that Stephens be permitted to wear the skirt-suit the firm requires for female employees, but did not appear to consider whether the company might be willing to accept some more gender-neutral attire.

“If a least restrictive means is available to achieve the goal, the government must use it,” wrote Cox, who was appointed by President George W. Bush. “This requires the government to show a degree of situational flexibility, creativity, and accommodation when putative interests clash with religious exercise. It has failed to do so here. The EEOC’s briefs do not contain any indication that the EEOC has explored the possibility of any accommodations or less restrictive means that might work under these facts.”

EEOC spokesperson Justine Lisser said her agency is considering its options for appeal. "We are disappointed with the decision and reviewing next steps," she said.

American Civil Liberties Union attorney Josh Block, whose group filed an amicus brief on the EEOC's side, said the implications of the ruling were troubling but he expects it will be overturned by a higher court.

"It would mean any religious employer would suddenly have a defense to firing someone in violation of any civil rights law as long as it was based on religious belief. … It's a very odd decision, and there are a million different ways it can and should be reversed," Block said.

Block said the ruling also showed that the dissenters in Hobby Lobby were right about the potentially sweeping impact of that decision.

“They specifically warned what the majority was doing would open up this Pandora's box,” he said. “The majority said, 'No, it won't.' This is a sort of a vindication of what the dissenters were saying all along.”