maybe the disconnect here is that you are harping on "the scientific method"
sure, if you want to say that science needs some prescribed "method" then you could argue that Bacon was the frontrunner there. but Francis Bacon has very little to do with christianity, and nothing to do with catholocism (if i remember that he was anglican correctly)
anyhow, i can tell that your argument is veering into that philosophy-oriented path that most science-illiterate religion people take. you harp on the philosophical stuff. like arguing Popper
the fact is that science doesn't care about whatever philosophers try to tell us should be our "method". harping on the "scientific method" is not at all what scientists actually care about. that's why we look to people who did real science, like archimedes and eratosthenes, and we do NOT look to idiots who rambled on endlessly about the "scientific method" like Bacon and Popper and a whole mess of non-scientists who wanted to opine on what scientists do without any first-hand knowledge.
if you want to look up references for what i am saying, Leonard Susskind has made a strong argument in favor of "scientists dictate what science is, not philosophers" so search that