Church courts of the Middle Ages had a deserved reputation for being far more lenient than their secular equivalents and this caused tension when the jurisdictions crossed. Henry II of England was particularly displeased about this in his dispute with the church that led to the murder of St Thomas á Beckett.
My two cents
There’s a lot of humanistic and antil-religious bias when it comes to the Middle Ages, with quips often written by people who have an axe to grind. Conversely, I like it when people bother to research and tell the other side of the story.
Peters, E. (2003). FAQ on the Inquisition. Available: http://www.bede.org.uk/inquisition.htm. Last accessed 20th Feb 2012.