If the source is an oligarchy, or in a court, senate, or ruler, then that source is the god of that system. Nothing more clearly reveals, in fact, the religions change in society than a legal revolution. When the legal foundations shift from Biblical law to humanism, it means that the society now draws its vitality and power from humanism, not from Christian theism. A church can be disestablished, and a particular religion can be supplanted by another, but the change is simply to another religion. Since the foundations of law are inescapably religious, no society exists without a religious foundation or without a law-system which codifies the morality of its religion.
Toleration is a device used to introduce a new law-system as a prelude to a new intolerance.
This is the background to the quote you saw. There is much more to theonomy than this. For example, most theonomists seem to eschew any attempt to abstract principles from Old Testament law. They would prefer to apply the laws as written. However, that is a discussion for another day.