Must science stick to methodological materialism?

Today's campaigning atheists are revisionists when it comes to explaining what science is, and how science works. That is, their theories and confident exclamations bear no real resemblance to the beliefs and practices of the fathers of modern science. They are instead after-the-fact just-so stories made up to support the atheist case.

One area in which this is particularly true is when atheists proclaim that "the scientific method is methodological naturalism". By that, they mean that science must always assume in advance that all causes and effects in the world that can be investigated are material causes and effects. Science must assume at the outset that the world is a closed system, entirely physical in its make-up - no supernatural, no divine design, intervention or intention in nature, no body-soul duality, etcetera. At the very least, it must say that these very ideas lie outside the realm of science and science cannot legitimately discuss them.

The fathers of modern science, and very many actual scientists as opposed to campaigning atheists-cum-scientists, believed quite the opposite. They assumed at the outset that the physical universe was the product of an orderly mind and designed with a deliberate purpose. This is what makes the idea of scientific investigation rational - we believe that there's something there to investigate, not just random chaos. It was in Christian Europe that modern science arose, amongst European Christians and those retaining the Christian assumptions. The universe was believed to be comprehensible by human minds, because human minds were thought to be made in the image of the divine mind responsible for the universe.

There is some overlap between saying "we expect an orderly world" and the concept of "methodological naturalism", because the latter expects things to work in a cause-and-effect way. Nevertheless, the only reason to adopt the concept of methodological naturalism is because we already hold to a concept of philosophical naturalism - i.e. because of our religious position. Otherwise, it is simply an unprovable philosophical bias that has no more right than any other to dictate what science can and can't do. To exclude certain concepts and explanations in advance is not science at all, much less the essential essence of science - it is religion.

I think it's enough for now to point out that certain sciences would be entirely ruined were they to actually stick to this rule. When an archaeologist digs up some pots and necklaces, what does he deduce? Should he be forbidden, in advance, from even considering that this might have something to do with intelligent human activity? Must he be forced to either choose the option of coming up with an entirely natural explanation for their formation, or being left to say  "as of yet we don't know, and must be humble until we get more data"? Unless we've lost our minds, it's obvious that this rule if applied at all would be the very death of archaeology. Archaeology begins with the assumption that such artefacts are prima facie evidence of human activity, until proved otherwise. In other words, it assumes the very opposite of what the atheists say is the very essence of science. That tells you all you need to know.