There is no single "scientific method" to speak of. Your epistemic position is ultimately just as faith based as you claim faith in God etc. is, the sciences (plural) just have a set of operations which, as you point out, seem to have practical utility and seem to be better than certain alternatives for building up shared epistemic structure.

The attitude of "we can't do better" is precisely the kind of attitude that would have hampered the creation of various sciences and their methods in the first place, and the production of scientific thought is often not as pure or logically consistent as all the methodological purists or Popperians seem to believe it is. Feyerabend, Quine, Von Foerster, Dataon and Gallison and several others have made this pretty clear and make the argument pretty forcefully in my opinion.

All sciences carry an ontology and value system along with them. Religion is also a rich and highly effective epistemic structure when your underlying ontological assumptions, values, and goals differ from those established and implicit in the scientific (predominantly utilitarian) Western enlightenment value system. Science is not able to found itself on some irrefutable bedrock "truth" correspondence any more than religion is. There is no basis by which we can actually solidify empiricism as somehow more privileged and more capital T true if we admit the possibility of human error.