The Inquisitions were responsible for about 3000 deaths over 400 years. For comparison about 10,000 clergy were killed in the Terrors around the French revolution in a few weeks (by atheists). Two thirds of those deaths were deaths in custody, not executions, which when you think of the conditions in medieval dungeons it's not that surprising. Most burning at the stakes were effigies of people who had died in custody, and the remainder were garroted before the fire was lit.
The inquisition only had jurisdiction over Catholics. If you said you weren't Catholic, they would release you - probably to other authorities who may have done worse to you, but the point is it was about determining whether people were true to the faith.
The Spanish Inquisition was all about figuring out who was really Catholic and who were Jews and Muslims lying about being Catholic so they wouldn't get expelled from Spain by the King.
It has the worst reputation in English speaking countries. Most early English language histories about it were written by British or American protestants - and it's not like they were often at war with Spain, or had a bone to pick with Catholicism.