The reason there's few in the Middle Ages is that the Witch hunts is actually a consequence of the rise of the institutionalisation of science in the modern age.

While folk remedies and popular midwifery was perfectly acceptable in the Middle Ages, when the reign of reason started, anything that didn't fall into the category of a science started to be frown upon then completely condemned. The result is that the science held by groups of women became severely suspicious, hence the witchcraftery accusation.

The initial targets of witchcraft accusation were not of religious nature. As I mentioned about Montaillou, in the 1300s the Inquisitor didn't take such accusation seriously and brushed it aside as just something completely unimportant.

I have yet to find any serious trace of paganism in Western Europe at that time. We're talking about areas that had been christianized a thousand years before. Remnants of pagan cults did linger in the High Middle Ages, but aside from fiction, I've not seen any evidence of such surviving cults in the late medieval period in Western Europe.