You've written a very dense post -- there's a lot to consider here.
The idea of natural law can be thought of as a positive thing (i.e. we all innately know that some things are good/bad) or a negative thing (e.g. a Lord of the Flies-type environment). In either case, it is separate from positive laws; in other words, the laws on the books may be based in "natural law," but the two are separate entities.
This leads to my question: What did Holmes think should be the basis of positive law, if not natural law -- utilitarianism? libertarianism?