Heresy was basically treason. Treason is still a capital offense. Should the Church have refused to act as fact-finder and judge? Maybe, but things were usually a lot worse when the Church wasn't involved since Inquisitors were supposed to have stuff like evidence, which wasn't as big a deal for civil law enforcement. Which is why more than a few accused criminals would try to commit heresy before their trials so that they could have them removed from the civil court to the Inquisition.
If you just mean that the Church being involved in the death of a person because of what they believed, then I do think numbers matter. When you have an organization so big with so many people involved, you expect crimes and evils and other badness. That is an unfortunate part of all those dark intellects and weak wills in action. Attempts to inflate the instances of these evils to absurdly impossible levels (millions being burned at the stake eg) for the purpose of gaining points in an argument is just dishonest.