Good history, done with consideration and taking into account the judgements and morals of that contemporary society, is almost never the black and white of much of current 'knowledge!' Shades of gray from white to black as we see the trend of various forces and societal movements played out on the stage.
Few people today understand the 700+ year "Reconquista" of the Iberian Peninsula and its effect on the Spanish and Portuguese societies and only decry what they see as the crimes against the Moriscos and the Jews lumped under the "Spanish Inquisition" and other actions. Having the gift of the "New World" following the end of Moorish Spain did give what seemed like God's gift of unlimited wealth and eternal prosperity to those shared countries as reward for their long struggle. These Universities you cite were some of the best of the results indeed.
As modern day specialists have shown, there is no doubt but that in a number of spheres (in dealing with sorcerers, blasphemers, writers, etc.) the Spanish Inquisition showed itself much more moderate and understanding than the civil courts(parliaments, provosts, bailiffs)in other European countries.
"The 'black legend,' as Pierre Chaunu stated, was only 'a cynical tool of psychological warfare' up to the time of the Renaissance and the classical period. Yet it is the foundation on which all the usual presentations of the Spanish Inquisition are based."