Your also source claims the medieval inquisition persecuted Jews and burned some at the stake in one incident 1288. Now I'd like to see some documentation of this, because I've read quite a bit about the inquisition and have never seen this incident mentioend. But even if it is true, it's just one incident in hundreds of years, hardly representative of the institution.
That was only the begining ...
"Much has been written of the inhuman cruelty of Torquemada. Llorente computes that during Torquemada's office (1483-98) 8800 suffered death by fire and 96,54 (sic) were punished in other ways (Histoire de l'Inquisition, IV, 252). These figures are highly exaggerated, as has been conclusively proved by Hefele (Cardinal Ximenes, ch. xviii), Gams (Kirchengeschichte von Spanien, III, II, 68-76), and many others. Even the Jewish historian Graetz contents himself with stating that "under the first Inquisitor Torquemada, in the course of fourteen years (1485-1498) at least 2000 Jews were burnt as impenitent sinners" ("History of the Jews", Philadelphia, 1897, IV, 356). Most historians hold with the Protestant Peschel (Das Zeitalter der Entdeckungen, Stuttgart, 1877, pp. 119 sq.) that the number of persons burnt from 1481 to 1504, when Isabella died, was about 2000...." - New Advent (Roman) Catholic Encyclopedia, Fray Tomás Torquemada - http://www.newadvent.org/cathen/14783a.htm
"And on the Medieval Inquisition page, the same New Advent (Roman) Catholic Encyclopedia told us that the "most active period of the institution" was when 5 of 24 'convicted' during a 7 year period, and 42 of 930 'convicted' during a 16 year period, were burned in the early 14th century. But here we have, by the most conservative (Roman Catholic) estimates, "about 2000" executed over a period of 25 years. That is a best case scenario average of 80 each year, or 1 every 4.5 days - for 25 years! And, since these numbers only take into account those for which records exist, it's likely that the true numbers are higher. David A. Plaisted makes a compelling argument that the true numbers exceed 50 million. And these are the doings of those who claim that they are the descendants of the apostles, and the infallible vicars of Christ." - http://jmgainor.homestead.com/files/PU/Inq/si.htm