I'm honestly not sure (but am willing to speculate) on the fact that alchemy and hermetic magic were more tolerated then hedge magic. I'm inclined to think that Alchemy was more male oriented, and was oriented toward the nobility.

I also have to wonder how much of the "stepping stone to science" could have also come from hedge magicians and herbalists...if their knowledge hadn't been discounted. Not that I'm going to get into the "male science vs. female science" nonsense, but I'm sure there was a lot of knowledge that was lost through being dismissed.