On June 28, the Senate Judiciary Committee began hearings on Elena Kagan’s Supreme Court nomination. On the same day, the Court announced its decision in Christian Legal Society v. Martinez. The coincidence was appropriate, because there was a striking complementarity between that ruling and a major controversy in Kagan’s career.

In Martinez, a 5–4 majority upheld the decision of UC–Hastings College of the Law, in San Francisco, to marginalize a group of Christian law students. As it happens, several years ago Kagan led a failed effort to marginalize the American military on the campus of Harvard Law School. The fact that Harvard failed where Hastings succeeded may point the way toward a rectification of the wrong that was committed in the Martinez case.

In the early 2000s, several elite law schools — including Harvard — denied the U.S. military permission to recruit on their campuses, in protest of the congressional prohibition on military service by open homosexuals. Congress responded by strengthening and clarifying the Solomon Amendment, which since 1996 had required access to campus for military recruiters as a condition of the receipt of federal funds.

Some of the affected law schools sued the federal government, claiming that the Solomon Amendment infringed their rights of “expressive association,” and lost 8–0 in Rumsfeld v. Forum for Academic and Institutional Rights (2006). The Supreme Court held that there had been no imposition of an “unconstitutional condition” on the grant of federal funds. The Solomon Amendment worked indirectly, with the “carrot” of federal funding, but the Court noted that Congress could even use the “stick” of directly requiring institutions, public or private, to be open to military recruiting, under its Article I power to raise and support military forces.

Yet this June, the UC–Hastings College of the Law was permitted to deny the campus’s Christian Legal Society (CLS) recognition as a registered student organization, which would have afforded it access to facilities and other resources. The group’s offense? Requiring members and officers to sign a “statement of faith” and abide by traditional Christian morality, which permits sexual relations only between husband and wife.

In explaining their refusal to recognize CLS, the only group ever denied such recognition, Hastings administrators at first claimed they were following university policies that prohibit discrimination based on religion or sexual orientation. But other student groups were permitted to base membership on shared ideas, and under existing precedents, CLS’s right to associate freely was likely to outweigh the school’s nondiscrimination policy. In short, the school was vulnerable to a charge that it was discriminating on “viewpoint” grounds — denying free-association rights only to these Christian students — so the administration scrambled to redefine its policy and its argument.

The school then claimed that it had an “accept all comers” policy (of which no one had previously heard), which allowed no student group to forbid membership to anyone. On this absurd basis — which would force a group of student Republicans to admit Democrats, or allow the Christian group known as “Jews for Jesus” to take over the campus Jewish group — the Supreme Court sanctioned the law school’s “diversity”-friendly hostility to the Christian Legal Society.

Justice Samuel Alito, in a powerful dissent, noted that the law school’s true policy was “accept-some-comers,” for registered groups were allowed to employ “conduct requirements” rather than “belief” to police their membership. The school had shed no light on what conduct standards could be used — although given its transparent effort to freeze out CLS, Alito said, “presumably requirements regarding sexual conduct” would be forbidden.

Yet the real calamity of the Martinez ruling, as Alito also noted, is not the prospect of hostile takeovers of small and politically incorrect groups. It is that students who are serious about their faith will, for the sake of their own integrity, simply not attempt to organize as a recognized group: “There are religious groups that cannot in good conscience agree in their bylaws that they will admit persons who do not share their faith, and for these groups, the consequence of an accept-all-comers policy is marginalization.”

The Supreme Court’s decision did not settle the matter completely: The Christian Legal Society may still prevail at Hastings if it can show on remand in the lower courts that the law school’s policy is selectively enforced and not really viewpoint-neutral. But Justice Ruth Bader Ginsburg’s opinion for the majority in Martinez shows the way for institutions of higher education to squeeze conservative religious student groups until they either drop their organizational efforts or dilute their devotion to the tenets of their faith. Colleges and universities need only declare a free-for-all in the world of student organizations, allowing any student to join and participate in any group, and count on the most fashionable views — or the emptiest and most innocuous ones — to prevail. Not just Christian groups, but Jewish, Muslim, and other religious student groups are put at risk by the Martinez ruling.

Now look at Elena Kagan and Rumsfeld v. FAIR. Dean Kagan and her allies lost, where Hastings won, because a statute specifically required them to give access to military recruiters or lose funding. A similar approach could effectively right the wrong of Martinez: Republicans and Democrats who respect religious freedom could pass a law that denies federal funding to universities that require student religious groups to compromise their commitment to their faith for the sake of official recognition.

Certainly in the case of public universities, this indirect policy would impose no “unconstitutional condition,” since Congress may even act directly to protect religious freedom against infringement by public-sector institutions. And a good case could be made for applying a similar policy to nonsectarian private-sector institutions, which enjoy nonprofit status under federal law and ample largesse from the federal treasury.

Justice Alito called Martinez “a serious setback for freedom of expression.” He might have said more pointedly that freedom of religious expression and association, a subject of special solicitude in the Constitution, was dealt a savage blow. But the rights the Court refused to protect — to organize based on faith and morals and to inhabit the public square alongside other groups in fidelity to one’s beliefs — can and should be protected by Congress. Will congressional leaders — and the White House — deny such protection to believers and cling to a “diversity” agenda that is increasingly being exposed as the imposition of ideological uniformity? Let’s find out.

— Mr. George is McCormick Professor of Jurisprudence and director of the James Madison Program at Princeton University. Mr. Franck is director of the Simon Center on Religion and the Constitution at the ZUMA Witherspoon Institute in Princeton.