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from the article: " Few people recall that that almost maniacal rebellion against Catholic teaching and, for that matter, commonsensical and civilized living was the trigger for the much-misunderstood Inquisition."

Speaking of "maniacal":

"The crusader army came under the command, both spiritually and militarily, of the papal legate Arnaud-Amaury, Abbot of Cîteaux.
In the first significant engagement of the war, the town of Béziers was besieged on 22 July 1209.
The Catholic inhabitants of the city were granted the freedom to leave unharmed, but many refused and opted to stay and fight alongside the Cathars.
The Cathars spent much of 1209 fending off the crusaders.
The Béziers army attempted a sortie but was quickly defeated, then pursued by the crusaders back through the gates and into the city.
Arnaud-Amaury, the Cistercian abbot-commander, is supposed to have been asked how to tell Cathars from Catholics.
His reply, recalled by Caesar of Heisterbach, a fellow Cistercian, thirty years later was 'Caedite eos. Novit enim Dominus qui sunt eius.'—'Kill them all, the Lord will recognise His own.'[53][54]
The doors of the church of St Mary Magdalene were broken down and the refugees dragged out and slaughtered.
Reportedly, 7,000 people died there.
Elsewhere in the town many more thousands were mutilated and killed.
Prisoners were blinded, dragged behind horses, and used for target practice.[55]
What remained of the city was razed by fire.

Arnaud-Amaury wrote to Pope Innocent III, 'Today your Holiness, twenty thousand heretics were put to the sword, regardless of rank, age, or sex.'[56][57]"

In another report:

"When Innocent III's diplomatic attempts to roll back Catharism[1] met with little success and after the papal legate Pierre de Castelnau was murdered (allegedly by an agent serving the Cathar count of Toulouse), Innocent III declared a crusade against Languedoc, offering the lands of the schismatics to any French nobleman willing to take up arms.

"An estimated 200,000 to 1,000,000 people were massacred during the crusade.[2][3]
The Albigensian Crusade also had a role in the creation and institutionalization of both the Dominican Order and the Medieval Inquisition. "

But at least there were no gas chambers, or crematoria, so it's all cool, right?

Agreed. Although a good bit of this version of history is distorted in the service of anti-Catholicism, just as that of the article is to be pro-Catholic.

We don’t really know what the Albigensians taught or believed, since about all we have of them is what their enemies, who exterminated them, said they taught and believed.

Their attitudes towards marriage and sex, for instance, might make a good deal more sense if we had their explanations as to why they believed as they did. Every religion looks like lunacy to outsiders, especially without an explanation of this type. Then most (not all) at least have an internal logic.

It is, however, indisputable that truly appalling atrocities were committed in crushing the Albigensians, and that the Catholic faith imposed on Europe by force did little to prevent awful tragedies and crimes.

http://en.wikipedia.org/wiki/Gilles_de_Retz

The common punishment for city’s which resisted sieges was to put much or all of the population to the sword. Sad, but true. The punishment was considered a way to stop endless warfare. Cities would be too afraid to all resist and drag out what would have been short wars - wars were only conducted for a matter of weeks usually because bad weather and the harvest season made the campaign season so short.

Also, there is no actual contemporary evidence that anyone said: “Kill them all, the Lord will recognise His own.”

The Albigensians were a bizarre, murderous, perverted sect. I can’t say it was bad that the crusaders wiped many of them out. The remnants were reconciled or went underground to be routed out and either reconciled by the inquisition or executed by the state.

But at least there were no gas chambers, or crematoria, so it's all cool, right?

If you want a good book on the Inquisition and and antidote to the Catholic propaganda, read:

The Friar of Carcassonne: Revolt Against the Inquisition in the Last Days of the Cathars

The inquisition was like a 14th century stasi, where people routinely made false accusations against rivals in order to eliminate them or take their property.

When the peasantry revolted and started assassinating the inquisitors, the dead clerics were declared "saints"