Cardinal Donald Wuerl, the Archbishop of Washington, acknowledged Friday that the Supreme Court ruling legalizing gay marriage creates tough choices for groups motivated to service by their faith. AFP PHOTO/JIM WATSONJIM WATSON/AFP/Getty Images (Jim Watson/AFP/Getty Images)

Legal experts on Friday said the Supreme Court’s ruling legalizing same-sex marriage could have a sweeping impact on religious conservatives from faith-based universities and nonprofit groups who are major government partners in providing social services to individuals, including county clerks and people in the wedding industry who oppose the celebration of such unions.

The tension between gay rights and religious liberty has been brewing for years as gay equality has spread, and Friday provided no clear solutions, because the court wasn’t considering specific questions of religious freedom. However, both sides have acknowledged in the case that the two are linked, and that faith-based groups will probably have to choose between tax-exempt status or government funding and upholding their view of marriage.

Some experts said that the majority opinion was respectful toward religion — a tone that could help down the road.

“Many who deem same-sex marriage to be wrong reach that conclusion based on decent and honorable religious or philosophical premises, and neither they nor their beliefs are disparaged here,” the majority opinion says.

But some saw a shrinking of the place of religion — and a potential threat to partnerships in areas from foster care to homeless shelters to hospitals.

“The majority graciously suggests that religious believers may continue to ‘advocate’ and ‘teach’ their views of marriage,” Chief Justice John G. Roberts Jr. wrote for the minority. “The First Amendment guarantees, however, the freedom to ‘exercise’ religion. Ominously, that is not a word the majority uses.”

Roberts raises questions other legal experts have agreed are likely to come up — such as religious adoption agencies that won’t place children with same-sex married couples or religious colleges that provide married housing only to opposite-gender couples.

During the Supreme Court’s oral arguments in March, Justice Samuel A. Alito Jr. compared the case to one involving Bob Jones University, a fundamentalist Christian university in South Carolina. The Supreme Court ruled in 1983 that the school was not entitled to a tax-exempt status if it banned interracial marriage.

Solicitor General Donald B. Verrilli Jr., arguing for same-sex couples, agreed that tax-exempt status is “certainly going to be an issue.”

Roberts wrote Friday that “There is little doubt that these and similar questions will soon be before this Court. Unfortunately, people of faith can take no comfort in the treatment they receive from the majority today.”

University of Virginia law professor Douglas Laycock, an expert on religious liberty, predicted “political gridlock” in the states, where the battles would continue. That’s because most states have just one or the other: modified anti-discrimination laws to protect LGBT people or religious-liberty protections, and they tend to enflame advocates when they come into conflict. The differences generally break along red-blue lines.

On Friday, Laycock said he doubted that faith-based groups will lose their tax-exempt status. but he predicted they will not be able to continue to receive government funding while discriminating against gay employees.

“The gay rights side keeps escalating its demands and public opinion keeps shifting in their favor,” Laycock said. “Conservative believers are their own worst enemies and lead people to think they are hateful morons, so they’re not getting much sympathy. . . . I think they’ll be faced with a choice: Either hire employees who openly flout [the organization’s] religious teaching, or give up government contracts.”

Both sides would suffer, Laycock said. “It’s a huge problem for religious organizations, who rely on funding, but it’s a problem for the government, too,” he said, noting the enormous share of social services provided by faith-based groups.

The issue could affect a wide range of groups and individuals, from massive social-service organizations such as Catholic Charities and World Vision to cake bakers, florists, disc jockeys or public officials involved in the marriage process.

Religious conservatives have become increasingly concerned about these issues. They hold up examples such as the Catholic Archdiocese of Washington’s Catholic Charities, which a few years ago ceased its foster care with the city after the District legalized same-gender marriage, saying the new law left it no choice. The charity also stopped providing health-care benefits to spouses of new employees rather than be required to extend them to same-sex spouses.

On Friday, Cardinal Donald Wuerl, the archbishop and a close confidante of Pope Francis, acknowledged there were tough choices for groups motivated to service by their faith.

“We must find a way to balance two important values, the provision of appropriate health care benefits for all Church personnel including their spouses, and the avoidance of the perception that by doing so we accept a definition of marriage and spouse contrary to faith and revealed truth,” he said in a statement.

Earlier this month, Alliance Defending Freedom and the Southern Baptist Convention’s Ethics & Religious Liberty Commission released a guide to help religious institutions avoid lawsuits including sexual orientation and gender identity.

House and Senate Republicans last week introduced a bill that would prevent the federal government from withholding tax-exempt status, contracts or accreditation from religious institutions that oppose gay marriage.

John Inazu, a law professor at Washington University in St. Louis who focuses on church-state issues, said the conflict is still unfolding.

“The federal government is not going to move tomorrow to strip tax exemptions for colleges and institutions. That’s not in the cards right now, politically or otherwise,” Inazu said. “The downstream consequences are still going to be in the crosshairs in the coming years.”