Interesting essay from an informational perspective...but frankly, in terms of what you find enjoyable in literature as demonstrated by said essay, I think you should step far away from the fiction section and remain within the safe, comforting confines of Dewey's decimals.
If 'spirituality' is a catch-all dumpster for 'a common explanation toward things I cannot show empirically at this very moment,' then the criticism is correct: this is a useless discarding of knowledge.
On the other hand, if you don't start with an assumption of first principles, you have no science at your disposal. Certainly, new knowledge can build upon established knowledge; but what did that knowledge build upon? Sooner or later, we must come up with a blank. No question can be asked, and tested, unless it starts with something to build upon. The scientist who says "I believe God did it; so how is it put together, and what can cause its condition to change?", is hardly incapable of making honest and useful observations about what s/he finds, nor -- at that broad of a level -- is s/he particularly different from the scientist who says "I have no God; so I'll investigate it, and ascribe its origin and operation to a chain of mechanisms that I was not around to observe, and which must ultimately go backwards to infinity."
It is also worth reiterating, as others have noted, that no man on earth has empirically proven everything he believes to be accurate (unless, perhaps, he is of an extraordinarily shallow and uncurious intellect). Time is on no-one's side; sooner or later, you must take someone else's word for it. The moment you are clutching your chest in agony is not the time to go enroll in a medical school's cardiology program, for example. You have a good-faith reason to trust in the surgeon's knowledge. Nor is the surgeon obligated to explain all of his knowledge and proofs to you at that moment, and you won't get past the mortuary by demanding otherwise. You can accept or decline the offered help on the basis of what you do know about your predicament; the wise man simply accepts the help and sets aside all other questions until a better time.
Which could be extended into a very interesting discussion of 'religious' faith, or more correctly who or whom you place your faith in (Jesus Christ? Buhdda? Mohammad? Someone else?), and what that person's credentials are to require it of you. Even better, it would be a discussion that does not plead to the rationality of being willfully ignorant of things that one cannot personally, empirically prove right now. No human really lives that way, nor can anyone do so. Death will come first.
Of course, Galileo was trying to understand how things worked. He wasn't trying to write escapist fiction.