The English common law tradition of religious toleration, which we inherited, has always had a problem with religious institutions that are not houses of worship—i.e. that are geared to ends other than the practice of religion itself. To (vastly) oversimplify for a moment, that tradition began (in the 16th century, and in some respects even earlier) with the aim of protecting Protestant dissenters and Jews but (very intentionally) not protecting Catholics. And the way it took shape over the centuries in an effort to sustain that distinction was by drawing a line between individual religious practice (in which the government could not interfere) and an institutional religious presence (which was given far less protection). Because Catholicism is a uniquely institutional religion—with large numbers of massive institutions for providing social services, educating children and adults, and the like, all of which are more or less parts of a single hierarchy—this meant Catholics were simply not granted the same protection as others. Obviously the intent to treat Catholics differently has for the most part fallen away since then, but the evolved legal tradition is very much with us, and it is not a coincidence that it always seems to be the Catholic Church that gets caught up in these situations when the government overreaches.
The inclination to resort to an argument for “conscience protection” when this happens is quite natural and understandable—the language of freedom of conscience is the essential vocabulary of our legal tradition of religious liberty. But it is problematic in instances like this precisely because that tradition itself is problematic in instances like this. Does an institution have a conscience? Does it make sense to speak in highly individualistic terms like conscience when discussing threats to religious liberty in our civil society? Is it right to ask for individual exemptions—accepting as a narrow and revocable favor from the state a freedom that until now was understood as a broad restriction on the power of the state—when the question on the table is really the basic character of our society? – from “Religious Liberty and Civil Society” (2014)