I guess that that's what happened, and what's happening everyday... Newton action at a distance wasn't convincing enough, so others sought other, "deeper" explanations, among which most notable is of course general relativity. (And it's probably noteworthy that, from an "instrumental" point of view, its benefits were initially marginal...) The difference to me is between saying "the explanatory power of this current theory can (and will eventually) be outdone" and "being able to explain is a dimension of no importance in a scientific theory". Maybe that is Chomsky's concern, even though this instrumentalist attitude is far from new or unknown (think of Copenhagen (lack of) interpretation of quantum mechanics, and its (in)famous motto: "Shut up and calculate"!) If you are interested in this line of reasoning, I found David Deutsch ("The beginning of infinity") and Karl Popper ("Conjectures and Refutations") two passionate (and opinionated) voices!