Religious types have long worried a ruling in favor of nationwide same-sex marriage could lead to the revocation of rights and privileges for religious organizations. During the arguments in Obergefell v. Hodges—the case in which the Supreme Court today ruled that gay couples "may exercise the fundamental right to marry" in any state—there was an exchange that lent some credence to those fears.

Justice Samuel Alito cited Bob Jones University vs. the United States, a 1983 decision allowing the federal government to strip a Christian university of its tax-exempt status for discriminating against interracial couples.

"In the Bob Jones case, the Court held that a college was not entitled to tax­exempt status if it opposed interracial marriage or interracial dating. So would the same apply to a university or a college if it opposed same­-sex marriage?" he asked.

Responded the solicitor general: "You know, ­­I don't think I can answer that question without knowing more specifics, but it's certainly going to be an issue. I don't deny that. I don't deny that, Justice Alito. It is going to be an issue."

Today, some wonder whether the Court just opened the door for the government to withhold tax or other benefits from private, faith-affiliated organizations that refuse to perform gay weddings, offer housing to gay couples, etc. From a recent article in The New York Times:

Conservative religious schools all over the country forbid same-sex relationships, from dating to couples' living in married-student housing, and they fear they will soon be forced to make a wrenching choice. If the Supreme Court this month finds a constitutional right to same-sex marriage, the schools say they will have to abandon their policies that prohibit gay relationships or eventually risk losing their tax-exempt status…as a violation of a "fundamental national public policy"… In a recent letter to congressional leaders, officials from more than 70 schools, including Catholic high schools and evangelical colleges, said that a Supreme Court ruling approving same-sex marriage would put at risk all schools "adhering to traditional religious and moral values."

Critics allege this is merely panic-mongering on the part of gay marriage opponents, noting that "there are religious denominations that ban women's ordination, and still have tax-exempt status."

But it's not clear that precedent is precisely relevant. By elevating marriage to a "fundamental right" in its ruling, the Court today gave it a special status that may not apply to, say, the right to be ordained a Roman Catholic priest.

The Supreme Court justices themselves disagree about what this decision means for religiously affiliated organizations. Writing for the majority, Anthony Kennedy offered assurances that people of faith would still be allowed "to advocate with utmost, sincere conviction that, by divine precepts, same-sex marriage should not be condoned." But John Roberts, the chief justice, warned in his dissent that protecting a right to "advocate" is not necessarily the same as guaranteeing one's freedom to "exercise" religion without reprisal.

Relevant sections from three of the opinions are below the fold.

From the Opinion of the Court:

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. But when that sincere, personal opposition becomes enacted law and public policy, the necessary consequence is to put the imprimatur of the State itself on an exclusion that soon demeans or stigmatizes those whose own liberty is then denied. … Finally, it must be emphasized that religions, and those who adhere to religious doctrines, may continue to advocate with utmost, sincere conviction that, by divine pre- cepts, same-sex marriage should not be condoned. The First Amendment ensures that religious organizations and persons are given proper protection as they seek to teach the principles that are so fulfilling and so central to their lives and faiths, and to their own deep aspirations to continue the family structure they have long revered. The same is true of those who oppose same-sex marriage for other reasons. In turn, those who believe allowing same- sex marriage is proper or indeed essential, whether as a matter of religious conviction or secular belief, may engage those who disagree with their view in an open and search- ing debate. The Constitution, however, does not permit the State to bar same-sex couples from marriage on the same terms as accorded to couples of the opposite sex.

From Roberts' dissenting opinion:

Federal courts are blunt instruments when it comes to creating rights. They have constitutional power only to resolve concrete cases or controversies; they do not have the flexibility of legislatures to address concerns of parties not before the court or to anticipate problems that may arise from the exercise of a new right. Today's decision, for example, creates serious questions about religious liberty. Many good and decent people oppose same-sex marriage as a tenet of faith, and their freedom to exercise religion is—unlike the right imagined by the majority— actually spelled out in the Constitution. Amdt. 1. Respect for sincere religious conviction has led voters and legislators in every State that has adopted same-sex marriage democratically to include accommodations for religious practice. The majority's decision imposing same-sex marriage cannot, of course, create any such accommodations. The majority graciously suggests that religious believers may continue to "advocate" and "teach" their views of marriage. Ante, at 27. The First Amendment guarantees, however, the freedom to "exercise" religion. Ominously, that is not a word the majority uses. Hard questions arise when people of faith exercise religion in ways that may be seen to conflict with the new right to same-sex marriage—when, for example, a religious college provides married student housing only to opposite-sex married couples, or a religious adoption agency declines to place children with same-sex married couples. Indeed, the Solicitor General candidly acknowledged that the tax exemptions of some religious institutions would be in question if they opposed same-sex marriage. See Tr. of Oral Arg. on Question 1, at 36–38. 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.

And from Clarence Thomas' dissenting opinion: