Natural philosophy and the groundings of science were extremely different in the Middle Ages compared to today, and things such as medical practices then were based off of notions which would be just plain laughed at today, but were seen as science then. Science such as what Lisa practices would be seen as odd even by other doctors, and easily heretical, even though it’s very much true that knowledge was lost - you can believe Lisa’s claims. Heck, different sects of the church were at each other’s throats. During the Dark Ages, a lot of things were unfortunately lost. Paranoia were rampant, and folk medicine healers, such as village wise women, were persecuted a lot.
You also need to bear in mind the line that the bishop says about Lupu’s former wise woman. She made allegations against Lisa, very likely from a mix of fear as well as jealousy. During witch trials often people would make accusations at others as a way to escape being tried as a witch oneself. The former wise woman likely had been accused herself, then having seen Lisa’s strange equipment, as well as wanting her old position back, pointed the finger at Lisa.
As for occultism and magic, any folk medicine could easily be misconstrued for witchcraft, regardless of it was or not. Wicca is not the correct term for it either, X - Wicca is a modern neopagan religion created by Gardner in the 1950s.