The Inquisition was hardly aimed at "wiping out" the Augustinian view of anything; any theologian is simply that, a theologian, with his insights which emphasize one area or the other, and which have to be understood within the totality of Christian doctrine and tradition. Hence it is that our current Pope is a big fan of St. Augustine. However, anyone can take one aspect of a particular theologian's work and overemphasize it, which could have been perceived as a danger.
Gratian was and is highly regarded and during his time was influential for his rather cynical political writings and philosophy. He had many enemies, and one of the unfortunate features of certain phases of the Inquisition was that it had ceased to be religious and was in fact being used by the Emperor or by various members of his court for attacking people perceived as political enemies.
The situation of the Jews was very complicated. They had been badly treated by the Visigothic kings who invaded Spain, who were initially followers of the Arian heresy, and compared to that were relatively well-treated by the Middle Eastern invaders. However, the Jews were first expelled by the Muslims themselves in the 12th century, although by the time of the Spanish Inquisition, many had returned and were settled in the Christian areas of Spain. Those who had remained in Southern Spain (by paying a very high tax or by converting to Islam) were indeed the very definition of dhimmis, and sympathized heavily with the Muslims. Even in towns where relative peace obtained (such as Toledo), the Muslims could not be trusted, and there were occasional attacks on the Christian population, attacks in which Jews participated as well. Later, when the Muslim leaders had been expelled, it was found that some of the Muslims who had been allowed to stay (mostly poor farmers) were plotting with Muslims from the Middle East to invade Spain again; in this case, it was also found that some of the dhimmified Jews who had remained in or returned to Southern Spain were supporting them with money and communications.
The Court of Ferdinand and Isabella was notable for the high presence of powerful Jews, not only conversos. Converso Jews were also very prominent in the Church, in city governments, etc. During the unification of Spain, the power struggles between local leaders, the rising middle class, and those allied with the King and representing central power became very acute. Jews were caught in the middle, and in many cases were perceived as representing the King and the central government. The decision was made to expel them only when the Queen felt she could no longer protect them, after anti-Jewish riots in some Spanish cities motivated by things such as the jealousy of city councilmen over the appointment of a Jew to some position or another.
My point is that the Inquisition did not exist in a vacuum. One may argue that its initial objective was not a bad one, since it sought to reestablish orthodox doctrine and authority in areas where they had become very corrupted. During the Muslim occupation, there were many areas that had not had resident bishops for centuries, and where the underground existence of Christianity had been supported by priests whose notions of Catholic teaching grew fuzzier and more distorted with every generation. In addition, there was considerable moral confusion, and many Inquisition processes were directed at clergy who were living immoral lives, teaching immoral doctrine, etc. The involvement of the State came about because the Church did not have the power to inflict civil penalties and therefore relied upon the State to do this part of it. And this was disastrous for the whole concept of an Inquiry directed at purifying and restoring the Faith.
It is undeniable that politics did get in and play a major part in the Inquisition, particularly in its later phase and even in its earlier phase in certain areas (under the inquisitor Torquemada, for example). The Pope himself issued bulls trying to stop the Inquisition in Spain, which were simply ignored by the Crown, which at that point had found it to be a useful tool having nothing to do with religion.
Interestingly, the Inquisition also functioned in the New World, and the great majority of the people punished by it were clergy, either for teaching syncretist heresies developed from their contact with native cultures, or for immorality, such as sexual abuse of indigenous converts.
I would agree. It's a mistake to think these were necessarily "evil" men bent on religious intolerance. There was a lot of stuff taking place on many sides.
People make the mistake of trying to judge people in the past by our current view of the world. We either soften history, apologize for it or try to explain it away. Instead we should just accept it as the way things were and not try to judge our forefathers. Their views were different than ours. I find these articles nothing more than a softening of historical facts.