What makes you think the Inquisition was a separate entity from the Catholic Church, as you seem to imply?

What is currently called the [Congregation for the Doctrine of the Faith][1] used to be called Congregation for Universal Inquisition (erected in 1542), which changed its name to Congregation of the Holy Office in 1908.

Also, a good book on the Inquisition, which dispels the myth that the Catholic Church executed people (it was the State who actually did that), is canon lawyer Ed Peters's [_Inquisition_][2]. There's also a good *Old Catholic Encyclopedia* article "[Inquisition][3]."


  [1]: http://www.catholic-hierarchy.org/diocese/dxcdf.html
  [2]: http://www.worldcat.org/title/inquisition/oclc/18683092
  [3]: http://www.newadvent.org/cathen/08026a.htm