Justice Alito agreed with the judgment but would have overruled Smith. He argued that Smith wrongly discarded nearly four decades of precedent applying heightened scrutiny to substantial burdens on religious exercise, and that it leaves religious minorities vulnerable whenever the government adopts a formally neutral, categorical prohibition.
He maintained that the Free Exercise Clause's ordinary meaning protects against government action that forbids or hinders religious practice, not merely against formally unequal treatment. In his historical account, founding-era guarantees of religious liberty broadly protected religious exercise, often subject to exceptions for threats to public peace or safety; those limits, he argued, presupposed that at least some exemptions from otherwise general laws were constitutionally required.
Justice Alito also argued that Smith was poorly reasoned, inconsistent with both earlier and later precedent, and unworkable. Its exceptions for individualized exemptions and so-called hybrid rights have generated doctrinal confusion, while courts have struggled to identify religious targeting, proper secular comparators, and the scope of permitted exceptions. Federal statutes such as RFRA and RLUIPA, he noted, have also shown that courts can apply compelling-interest review without the "anarchy" Smith feared.
The majority's contract-based ruling, in his view, was precarious because Philadelphia could eliminate its unused discretionary-exemption provision and renew its exclusion of CSS. He would instead hold that Philadelphia's action failed strict scrutiny even if its policy were neutral and generally applicable. CSS had never prevented a same-sex couple from becoming a foster parent, other agencies were available to certify such couples, and the City could not suppress CSS's religious practice merely because its traditional view of marriage was considered offensive.