Give me an instance of "philosophical supernaturalism?" You don't by any chance mean logic? That's pretty supernatural! Not a spot of the material to it! But science wouldn't get very far without it. Nor would philosophy for that matter.
If you don't like that terminology, what do you prefer? If methodological naturalism is not an acceptable basis for scientific inquiry because it is "derived from philosophical naturalism", what philosophy do you propose to derive a methodology from, and what would that methodology be?