The Inquisition was originally created in order to put a stop to the practice of local authorities using heresy cases for political purposes. The church was in the business of saving souls, not eliminating enemies. It got out of hand when combined with secular authority as in the case of the Spanish Inquisition.
That's how I understand it too. What I wonder is whether more people have been killed, lost property etc. without the Inquistion.
It looks like 800-5000 persons were executed by order of the Inqusition between 1478 and 1834.
Meanwhile, from 1450-1700 an estimated 8,000 to 26,000 persons were killed as witches in Germany alone.