You will say, by this rule, if some congregations should have a mind to sacrifice infants, or (as the primitive Christians were falsely accused) lustfully pollute themselves in promiscuous uncleanness, or practise any other such heinous enormities, is the magistrate obliged to tolerate them, because they are committed in a religious assembly? I answer: No. These things are not lawful in the ordinary course of life, nor in any private house; and therefore neither are they so in the worship of God, or in any religious meeting. But, indeed, if any people congregated upon account of religion should be desirous to sacrifice a calf, I deny that that ought to be prohibited by a law. Meliboeus, whose calf it is, may lawfully kill his calf at home, and burn any part of it that he thinks fit. For no injury is thereby done to any one, no prejudice to another man’s goods. And for the same reason he may kill his calf also in a religious meeting. Whether the doing so be well-pleasing to God or no, it is their part to consider that do it. The part of the magistrate is only to take care that the commonwealth receive no prejudice, and that there be no injury done to any man, either in life or estate. And thus what may be spent on a feast may be spent on a sacrifice. But if peradventure such were the state of things that the interest of the commonwealth required all slaughter of beasts should be forborne for some while, in order to the increasing of the stock of cattle that had been destroyed by some extraordinary murrain, who sees not that the magistrate, in such a case, may forbid all his subjects to kill any calves for any use whatsoever? Only it is to be observed that, in this case, the law is not made about a religious, but a political matter; nor is the sacrifice, but the slaughter of calves, thereby prohibited.
By this we see what difference there is between the Church and the Commonwealth. Whatsoever is lawful in the Commonwealth cannot be prohibited by the magistrate in the Church. Whatsoever is permitted unto any of his subjects for their ordinary use, neither can nor ought to be forbidden by him to any sect of people for their religious uses. If any man may lawfully take bread or wine, either sitting or kneeling in his own house, the law ought not to abridge him of the same liberty in his religious worship; though in the Church the use of bread and wine be very different and be there applied to the mysteries of faith and rites of Divine worship. But those things that are prejudicial to the commonweal of a people in their ordinary use and are, therefore, forbidden by laws, those things ought not to be permitted to Churches in their sacred rites. Only the magistrate ought always to be very careful that he do not misuse his authority to the oppression of any Church, under pretence of public good.
The application can be tricky (that’s the fun thing about pretences, some of them can be quite convincing, especially to the motivated reasoner); but it’s hard to argue with Locke’s basic “If it’s forbidden for reasons claiming ‘but it’s my religion!’ confers no exemption; while if there is no reason to forbid it the fact that it’s part of a filthy heathen’s religion doesn’t cut it as a compelling state interest” theory.