The New York Times was thinking ahead. On Thursday, before today's Supreme Court decision legalizing gay marriage nationwide, the Times ran a what-if story -- focusing on implications for conservative colleges that ban gay relationships.

The newspaper was less than sharp when the decision came out. But first, the good stuff.

In the Thursday story, the Times, which typically holds the towel for whoever is in the ring for liberalism, sounds almost sympathetic in citing conservative fears:

The religious schools are concerned that if they continue to bar gay relationships, the Internal Revenue Service could take away their tax-exempt status as a violation of a "fundamental national public policy" under the reasoning of a 1983 Supreme Court decision that allowed the agency to revoke the tax-exempt status of schools that banned interracial relationships.

In a recent letter to congressional leaders, officials from more than 70 schools, from Catholic high schools to 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."

"I am concerned, and I think I’d be remiss, if not naïve, to be otherwise," said Everett Piper, president of Oklahoma Wesleyan University, in Bartlesville, Okla. "This is not alarmist thinking. This is rational listening."

The Times goes into considerable detail about the leaders' fears. A "yea" ruling on same-sex marriage by the high court, the newspaper says, could force colleges to change their policies on married housing, benefits to spouses, even sexual intimacy on campus. Flouting federal orders could cost their tax exemption.

And the article doesn't just wave off the worries as paranoia. It cites a discussion in April between Supreme Court justices and Donald B. Verrilli, the U.S. Solicitor General. Key to that talk was the court's 1983 decision that revoked tax exemption for Bob Jones University, which had banned interracial dating and marriage. Justice Samuel Alito asked if a school could likewise lose its exemption if same-sex marriage were made a basic right. Verrilli demurred but didn't deny the possibility.

The Times gets the views of an impressive spectrum of experts and activists. They include presidents of conservative colleges and activist groups, as well as their more liberal opponents. I admired the story's attempt to nuance conservative concerns, then to nuance the nuances.

One expert says the Bob Jones decision has never been applied to anything but race, including sexuality. Another says that public officials would want to avoid appearing to oppress religious organizations. Still, the latter is a political argument, not drawn from "principle," as one law prof says. Ergo, it may be true in the short term, but future politicians may choose to go after religious schools.

The Times allows a bit of snark when Professor Douglas Laycock of the University of Virginia calls those who resist gay rights a "handful of crackpots." But his opinion is balanced by that of Eugene Volokh, a law professor at UCLA: He says that if he were a conservative Christian, he would worry "that within a generation or so, my religious beliefs would be treated the same way as racist religious beliefs are."

Unfortunately, the newspaper relapses into its habit of selective labeling. The story uses the "conservative" word five times, slapping it onto Vision America and the Family Research Council. But The Daily Show and Americans United for Separation of Church and State escape any adjectives, though they generally fall to the left of public opinion.

Worse is something the Times does not say: how the Supreme Court ruling will affect the free exercise of religion -- a First Amendment right, which the court majority ruling didn't mention either. The Thursday article talks a lot about rights -- gay rights, civil rights, the right to same-sex marriage -- but not about religious rights. The only exception is in reporting Senator Mike Lee's new bill, which he calls the First Amendment Defense Act. Nor does the Times' breaking news story address the matter.

Other mainstream media do bring it up. The Washington Post quotes from Chief Justice John Roberts Jr.'s rather sarcastic dissenting opinion: "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."

Reuters, too, quotes from Roberts' criticisms:

Although the ruling only affects state laws and religious institutions can still choose whether to marry same-sex couples, Roberts predicted future legal conflicts.

"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," Roberts said. Roberts gave as an example a religious college that provides married student housing only to opposite-sex couples.

And the nonprofit MinnPost in Minneapolis quotes Justice Alito on how the decision may harm religious freedom:

It will be used to vilify Americans who are unwilling to assent to the new orthodoxy. In the course of its opinion, the majority compares traditional marriage laws to laws that denied equal treatment for African-Americans and women. The implications of this analogy will be exploited by those who are determined to stamp out every vestige of dissent.

Some of those concerns, as you know by now, came out of the mouths of law professors and conservative Christians in Tuesday's Times story. But even there, rights apparently aren’t for religious conservatives. It's a big oversight not only for the nation's highest court, but also for what many see as the nation's dominant newspaper.