Madden's lecture series is a disgraceful, one-sided attempt to justify a thousand years of oppressive torture and execution on an industrial scale, to enforce total thought-control across all of Europe.
One can defend some of the Church's actions--in the case of witch-burnings, for instance, one can in some cases show that the Church's regulation of the inquisitorial process dampened the flames, preventing the population from taking matters into their hands and burning more people. And it's true that the papacy sometimes reigned in overenthusiastic inquisitors.
But there are also cases in which one can show that inquisitors took a zealous glee in torturing and executing far more people than the local populace or secular authorities would have; and the Goa Inquisition, which seems not to be on the curriculum, was 260 years of cultural genocide. (Okay, technically only 256.) And there are many cases when a vicious zeal in inquisition advanced a priest's career, such as the Dominican Antonio Ghislieri, who entered the priesthood specifically in order to become an inquisitor, and eventually became Grand Inquisitor and then Pope Pius V. He reportedly still liked to attend torture sessions even after becoming Pope.
There are no cases in which you can call any of the many inquisitions just or humane, since they only enforced unjust laws, and only by cruel methods. Nor can you defend it, as Madden does, by saying that getting rid of troublemakers was a normal, necessary process for all ancient governments. The Inquisitions were a use of legalized, systematic terror to enforce complete uniformity of thought--a phenomenon which never existed anywhere on Earth prior to 1000 AD, and is AFAIK unique to Christianity, the French Revolution, communism, Nazism, and contemporary academia. (There was an Islamic Inquisition, but it focused only on whether the Koran was created or eternal, and only lasted 15 years. Ancient Rome had only a few brief inquisitions, and only to find people who refused to offer sacrifice to the Emperor, not to enforce any beliefs.)
He makes the usual pathetic excuse that the Church didn't actually execute, or even want to execute, heretics; they were actually "protecting" the heretics from the state, who were the ones who would actually execute them, by giving them a chance to recant. He describes inquisitions in general as being dedicated to saving heretics from the mean old kings who would otherwise kill them. Thus ignoring the fact that inquisitors throughout the centuries spoke and wrote of condemning heretics to the flames; that the Church was not "protecting" heretics, most of whom the secular authorities never would have bothered; and that popes regularly ordered kings to exterminate heretics more vigorously from 1200-1600 AD, and threatened to excommunicate rulers who failed to execute heretics condemned by church inquisitions.
That was bad enough, but I reached my breaking point in lecture 5. As "one of the foremost historians of the Crusades in the United States", Madden has no excuse for making such a disgraceful, dishonest attempt to justify the Albigensian Crusade, one of the worst atrocities in history.
First he pretends that the clergy in Languedoc were too extravagant and corrupt to obey the virtuous Pope Innocent III, and this was why Catharism flourished; when in fact it flourished because the Papal court at the time was so extravagant and corrupt that the asceticism of the Cathars greatly impressed the people. Then he says that the Crusade "got out of control", even though the massacre at Beziers, in which the crusaders murdered the entire population of 20,000 men, women, and children, happened in 1209, and the crusade continued in that vein for another 20 years, under 3 popes, and the murderers received nothing but praise and commendation from the popes and their clergy. (The Beziers massacre was where the phrase "Kill 'em all, and let God sort 'em out" came from, said by the Pope's personal representative, Abbott Arnaud Amalric, who was in charge of the massacre.)
Maddens also claims the crusade was "never meant to exterminate the heretics" even though many missives, orders, and sermons about the crusade made during the crusade contain the phrase "exterminate the heretics" in them (I think the preferred phrase was "extirpandam haeresim"), and every account agrees that the Pope and the crusaders all demanded that all heretics be killed.
He never mentions that the crusaders set the policy that it was better to kill everyone in a city that was 99% Catholic than to risk overlooking a few heretics. He never mentions the main goal of the crusade for the Church: to enforce absolute submission to the Pope throughout Europe (a key theme in 13th-century European history).
Maddens never mentions the massacre of Beziers, or any other of the massacres of the Albigensian crusade. He pretends this crusade was unusual in being against Christians, when perhaps half of all crusades were against Christians. He does not mention the systematic policy of terror, torture, painful mass executions, and massacre used throughout the crusade. He merely says it was "bloody", with no mention of the fact that the vast majority of the blood was that of unarmed men, women, and children. The estimates of the number of civilians who died from violence, exposure, or starvation over those 20 years range from 250,000 to 1 million. We have a lengthy account of the crusade written by the Cistercian monk Peter of lex Vaux-de-Cernay, whose entirely sympathetic account of it nonetheless reveals that the crusaders, and the church backing it, were more bloodthirsty and cruel than the Taliban.
(He also never mentions that the extermination of Cathars began 100 years before the Albigensian Crusade was declared, or that it continued until 1826, when the last one was killed. Nor, oddly, does he ever touch on the Albigensian Inquisition itself, which began only after the end of the Crusade and went on for decades. Probably because there's not much nice you can say about decades of torturing people into confessing heresy and then burning them alive by the dozens or hundreds.)
Then he goes on to lie about the Waldensians. He pretends that Waldo was just some whacky uneducated man who didn't know anything about the Bible, and justifies this by saying that the Pope had theologians quiz him and then declare he was not competent to preach. Anyone who knows anything about the papacy in the high middle ages and the Renaissance knows that such papal tribunals always had a predetermined outcome. He also neglects mentioning that Waldo's objections to Catholic theology were based on his having read much of the New Testament, and were mostly the same as the objections later made by Protestant reformers, again based on reading the Bible and realizing that Catholic theology and practice were something quite different.
He neglects to mention that the Catholic church, knowing full well that their theology was only partly based on the Bible, had already tried to prevent the laity from discovering this by implementing a general policy, from 1079-1870 AD, of declaring unauthorized translation of the Bible into "vulgar" languages, or the reading of such translations by the laity--in many cases, the reading of any translations--as heresy, precisely because anyone reading the Bible would discover that Catholic doctrine was a patchwork of contradictory texts and neo-Platonist philosophy. This banning of the Bible was made official dogma at the 4th Lateran Council in 1215, and upheld by the Council of Tarragona in 1234, the Council of Trent in 1564, through Pope Pius IX's 1846 encyclical, and by Pope Leo XIII's Apostolic Constitution of 1897.
His later lecture on "The Roman Inquisition" is mostly one long argument, based on character assassination, biased summaries, and irrelevancies, that Galileo was a jerk, and the Catholic Church was perfectly reasonable and justified in putting him on trial for his life for promoting the Copernican solar system.