One of the most annoying thing my teachers tell me is, "Don't think too much." I've gotten from almost all my science and maths teachers. Heck, even my English teachers told me this when I began deconstructing essay questions.
So, you're right, science needs to take certain assumptions for granted. And yes, many questions are beyond the purview of science. To ask them within the science classroom is indeed "sacrilegious."
P.S. This is the first "philosophical" essay I've read from you. I'm impressed.