In the next few months, courts in New York and New Jersey will render decisions on whether the Constitution requires recognition of same-sex marriage. Proponents of same-sex marriage rest their case largely on claims of toleration. In a diverse society, their argument goes, government should not impose a particular and restrictive moral vision on the whole society.

This is a persuasive argument, even for people like me who are personally firmly opposed to same-sex marriage on religious grounds. Unfortunately, like the Puritans, who wished to be tolerated but wouldn’t tolerate others, proponents of same-sex marriage are unwilling to extend similar tolerance to those who find such arrangements immoral, and seek the right to order their own lives and institutions accordingly. In fact, where same-sex marriage becomes the law, religious groups that oppose same-sex marriage will find their freedom to operate in accordance with their beliefs severely challenged.

Of course, proponents of same-sex marriage acknowledge that clergy and churches cannot be compelled to perform same-sex ceremonies. But that concession is hardly an important one. It doesn’t resolve most of the religious liberty claims that are sure to arise from legalization of same-sex marriage. Already, the following cases are in litigation or have been posed by actual events:

• Catholic Charities in Massachusetts has lost the right to place children for adoption because it will not place children with same-sex couples. Gay rights advocates have rejected out of hand a proposal under which Catholic Charities would refer same-sex couples to other agencies placing children for adoption.

• A school district banned a t-shirt with a message calling gay sex immoral. (The shirt was worn in response to other students organized to defend homosexuality and proclaiming that message.) So far, the federal courts have upheld the school, and have been applauded in doing so by gay rights groups.

• In California, a Christian school has been sued for expelling two girls it asserted were in a publicly known lesbian relationship, a relationship at odds with the religious views the school seeks to inculcate. A trial court has refused to dismiss the complaint.

• A rabbinic group certifying a caterer as kosher is asked to lend its imprimatur to the catering of a same-sex commitment ceremony.

Future legal conflict is virtually certain with regard to licensing of psychological clinics, social workers, marital counselors, and the like, as groups (or individuals) seek licenses from the government or accrediting agencies to run facilities, professional practices or operate accredited schools in keeping with their religious beliefs. The American Psychological Association’s code of ethics regarding homosexuality excludes conservative Protestants, Catholics, and Orthodox Jews.

A looming question is the tax-exempt status of “para-church organizations” that oppose gay marriage. These are organizations run by religious groups other than actual houses of worship, such as social welfare organizations, international relief agencies, hospitals, homeless shelters, and schools. While the tax-exempt status of actual houses of worship will not be rejected, the courts will be pressed to treat para-church organizations differently. In practice, every large charity depends on the federal income tax and state real-estate-tax exemption. Under current law, the government may (and, some would say, must) deny exemptions to groups that violate fundamental public policies, such as anti-discrimination laws or laws recognizing certain relationships as marriage.

Support for marriage has long been viewed as part of the fundamental public policy of every state. When same-sex marriage is legalized, support for same-sex marriage will be fundamental public policy too. Will institutions that refuse to recognize such marriages lose their exemptions?

Tax exemption is just one example (albeit an important one) of a broader problem. The impact of same-sex marriage or civil unions on religious liberty is likely to be severe and pervasive. How severe and how pervasive depends on how prepared the champions of tolerance are to tolerate the rights of traditionally religious people who oppose same-sex relationships. So far the answer is “not very.”

The Free Exercise Clause as the Supreme Court currently reads it offers little or no protection for the onslaught of legal pressure that will come when state courts and legislatures legalize same-sex marriage as a civil right. If there is to be protection for religious liberty in a post same-sex marriage world, it will come from legislatures offering generous religious exemptions.

Not every religious liberty claim can (or even should) be vindicated in a world in which same-sex marriage is legal. Purely commercial enterprises such as hotels would not, for instance, be allowed not to make facilities available for same-sex couples. Doctors should generally not be allowed to refuse to treat patients in same-sex relationships. But tolerance is an odd banner under which the religious beliefs of millions of Americans, beliefs that have a long and considered religious history, are systematically swept away.

Tolerance ought to be a two-way street. A vibrant tolerance would allow for formal recognition of same-sex relationships and their acceptance in the secular economy and (as far as possible) the right of persons with moral and religious views to refuse to accept those relationships as valid in their own lives and institutions. In keeping with the current degraded status of American political debate, proponents and opponents of same-sex marriage each seek total victory. We would all be better off if, for once, the extremists did not capture the debate.

Mr. Stern is a New York attorney specializing in religious liberty and separation of church and state issues.