Notre Dame law professor Richard Garnett explains how we should think about and defend the liberty of religious institutions:
To embrace this idea as still-relevant is to claim that religious institutions have a distinctive place in our constitutional order—and not only a distinctively worrisome or harmful one. It is to suggest that churches are not “just like the Boy Scouts” and that, while they to a large extent function in civil society in the same way and deliver the same Tocquevillian benefits as any number of voluntary associations, they are, in the end, different.
True, it is increasingly difficult, within the boundaries of argument set down by some versions of liberal political theory, to justify, on principled grounds, special treatment for religious liberty. Still, in our history and tradition, “religious” institutions and authorities have acted, and have been regarded, as special and distinct, whether or not “religion” has been understood as neatly separate from “culture,” “conscience,” or “morality.” We live under a written Constitution that “singles out” religion and we inhabit a tradition in which “church” and “state” have, in a special way, cooperated and contended. If it is anachronistic to invoke the freedom of the church, it seems even more ahistorical to deny the distinctive (for better or worse) place and role of religious actors in that tradition, and today.