I was clerking for Justice Sandra Day O’Connor in 1990 when the Supreme Court decided Employment Division v. Smith—a case that has had an outsize effect on all subsequent debate over religious liberty in the U.S. Two drug counselors in Oregon had been fired after they used peyote, an illegal drug. They argued that because they used the peyote during a Native American Church service, the First Amendment’s guarantee of the “free exercise” of religion protected them from being penalized. The Supreme Court disagreed.

This...