Though I am a person of faith I have not always been, so I understand personally and grasp intellectually alternate philosophies/worldviews. I like to live life with a healthy intellectual openness, never assuming I have all the answers.
I don't have any problem with that version of faith (as described by Raphael).
Is science a superior ontology?
Probably. And that's because science is pragmatic. So, whenever there is a change, the pragmatism is likely to move to a better direction.
Note, however, that pragmatism tends to be subjective. So what one person sees as better, another may see as worse. We might say that science depends on the collective pragmatism of the scientists.
I might modify your statement from my perspective though, to "Any objective knower of truth is not testable or controllable by the scientific method."
This is why science should be described as pragmatic, and not as truth seeking.
Fundamentalism - the anti-American, anti-Christian branch of American Christianity