If you look carefully, you will notice that the techs that require SM are techs which religion would not help you with anyway. Biology? That requires acceptance of Evolution. Flight? If Man was meant to fly, God would have given him wings. Fission? I could spend a while on that one, but I don't have the hours to waste.
Sure, you lose a lot of science, but it was all haphazard. By using a specific methodology, you get better science, and hence better technologies. You have to dump your old infrastructure and build a new one, and doing that isn't cheap.
If questions end because the answer to every one of them is "God wanted it that way", then you can't advance your technology beyond the basics that you accidentally discovered along the way.