For consistency’s sake, proponents of methodological naturalism need to say that natural science, as distinct from metaphysics, is best done while bracketing the question of supernatural causation. That is, they should say that the best approach for science is to come up with testable theories that require no reference to the supernatural. From that viewpoint, it could well turn out that one can’t explain all natural realities in purely naturalistic terms. But that issue cannot be settled one way or another just by natural science. Methodological naturalism is just that: methodological, not metaphysical.
ID proponents would similarly do well to confine themselves to a negative approach. That is, they could and should point out the ways in which natural science, merely as such, fails to explain certain things. Thus “irreducible complexity” would be complexity that natural science, merely as such, does not plausibly explain purely as the product of other, natural entities and forces. The question whether natural science ever could explain such complexity as such a product would then become a matter of philosophical opinion. Scientists such as Michael Ruse are convinced that the methodology of natural science is equipped in principle to explain everything naturalistically, and other scientists such as Michael Behe are convinced that it is not. Both positions are legitimate within the scientific community, but neither is dictated by the methodologies of natural science.
The problem with the ID debate is that neither side, by and large, is willing to be modest enough. Each seems convinced that “science” supports their own position, when in fact it could support either. That's primarily why Judge Jones is wrong. But it's not sexy to say that. If people did take that approach, everybody would win, which means nobody would lose, which means nobody's ego would be stomped on and humiliated. And what fun would that be?