The truth is that Inquisition aim was exactly opposite: to stop chasing and burning innocent woman (and man) by all kind of petty lords and civil "courts" who used witchcraft accusation to get rid of opponents. This was done in the name of Catholic Church so Rome decided to do something about this and stop that practice by introduction of pretty modern standards of court proceedings - this way Inquisition was born.
Inquisition was punishing heavily those who gave false testimony and that cut number of witchcraft cases significantly.
In addition the punishment for heresy was rarely death penalty (about 1,5% of cases), which is less than 5 thousand executions during several centuries of Inquisition activity. Typical punishment was fasting, scourging or pilgrimage.
Coming back to Umberto Eco writing, he described in "The Name of the Rose" Dominican friar Bernard Gui as some bloody, mindless, cruel madman, medieval version of Doctor Mengele. While the truth was exactly the opposite - he was a decent and educated man.
Obviously historical research and facts are much less interesting than Eco pop writing, but we live in the pop age and believe in the pop "truths" so this is not a big surprise.