Here's the scenario: Spanish soldiers are sent to Holland by their king, who also happens to be the duke of Ghent and sovereign of other areas in Holland. They are foreign troops sent in to quell a rebellion.
They are attacked by partisans or militia from a local town. They roll into the town, don't speak the language, have little means of determining who's hostile and who's neutral. They kill all the men of fighting age, since they have no other practical means of neutralizing the threat.
This is certainly a war crime. It's despicable behavior. They shouldn't even be in a country that's not their own at war with people who have no quarrel with them personally. They're analogous to the Hessians in America during the Revolutionary War.
That's the human situation as it probably was on the ground: emperor's occupation forces march into a village that's offering guerrilla resistance and sheltering rebel troops. The occupiers kill all the menfolk. The way it reads to Fiske is this: Papist soldiers invade a righteous Protestant village and kill all the Godfearing men of that town whose only crime was to read their Bible. Chalk that up as 300 people executed for heresy by the Roman Church.
That's Fiske's spin - I'm not saying he's making it up (although he admits that 75,000 is a bit high), but that he's interpreting it in a sense amenable to his thesis.
As far as the Albigensians are concerned - the Catholic Encyclopedia does not say that the war was well and righteously conducted and the outcome was wonderful. It's more like: what if a few thousand Muslim fanatics took over a swath of southern Michigan and started instituting Sharia law and killing people who defied Sharia. Then the Michigan National Guard units come in - they're overzealous and kill a hundred thousand Muslims, killing fanatics along with many more who were just along for the ride. My reaction: it really is a shame about all those people who died who may or may not have sympathized with the jihad in Southern Michigan, but thank God those jihadis were stopped and they can no longer use America's heartland as a base of terrorist operations.
Substitute Albigensians for Muslims, the Languedoc for Southern Michigan and Christendom for America and you've captured the Encyclopedist's sentiment.
The Albigensian War wasn't pretty - but consider the alternative: a fanatical death cult conquering the heart of Europe.