And I've always said that the governing philosophical presuppositions of science are determined by the theoretical content of science, rather than the other way around. (Historically these presuppositions have always been modified to accommodate genuinely successful theories, as for instance with Newton's "occult" force of gravity. It violated the classical dictum of materialism: that force could only be transmitted by physical impacts between bodies.)
All you need is one important and manifestly successful scientific theory incorporating a "supernatural hypothesis" to change the ruling assumption of methodological naturalism. So go ahead and do "then a miracle happens" science. No one is stopping you. On the other hand no one will follow you in such pursuit either, unless and until you can show that it works. Ah, there's the rub.
Then you may be displeased to learn that you have made a mistatement. Here is what scientist Richard Lewontin said on the issue....
We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, and in spite of the tolerance of the scientific community for unsubstantiated just-so-stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is an absolute, for we cannot allow a Divine Foot in the door." - Richard Lewontin
Do you see? It is NOT the theory, facts or evidence that drives his rules. It is the philosophical presupposition. And unless you are a famous scientist like he is I'd say that he speaks for the community moreso than you do.
Look, I agree that what you say is the way it SHOULD be, but the guys you look to are doing it the OPPOSITE of the way you think it should be done.
As far as me proposing a "supernatural hypothesis" goes, many have been proposed and verified at least to the extent of their naturalistic counterparts. The trouble is not that we have failed to propose valid ideas- its that the Dr. R. Lewontins of this world refuse in advance to consider them. They would prefer the most outlandish naturalistic hypothesis to the most intitutive theistic one. And somehow they have sold otherwise smart guys like yourself on the idea that this constitutes "objectivity".
PS- Your example is anchronistic. Materialism was not even named before Newton and gravity. His theory was already part of the "natural world" long before the "classical dictum of amterialism" was ever codified.