What did they do to people who they thought were witches in the middle ages?

Answer 1

What I find is that there were insane asylums in the Middle Ages, but only people who were otherwise unmanageable were put in them. The Priory of St. Mary of Bethlehem started giving care for insane people in 1357, but there were very few patients until the after the Middle Ages ended. Long after the Middle Ages, the common name of this hospital provided the English language with the word "Bedlam," as it gained a reputation for brutal treatment of inmates during the 17th century.

I was unable to find any reference that supported the idea of insane people being killed.

I also checked about babies being killed, and it is true that in some legal codes of Germanic groups of the Early Middle Ages, a mother who killed a newborn infant could not be prosecuted, but I suspect this had more to do with post partum disorders and less with special needs infants had. The legal codes were unspecific about reasons, but the law only applied to the mothers.

There is a link below to the medieval section of an article on the history of psychiatric institutions.

Answer 2

In many places, such as the Carolingian Empire, they left people thought to be witches alone because there were laws against believing in witches. There were also laws making burning witches a capital crime. In some other places, there were laws against witchcraft, and the laws varied on this. There was an increase in the numbers of people prosecuted for witchcraft in the Late Middle Ages, but the bad witch hunts came later, after the Middle Ages ended.

Please see the link below.