As for the proportion you mention, it is by a lot smaller than the killings of the XX century (in Russia and China, for instance).
Anything can be dismissed as anti-Catholic propaganda. At the same time, I found the ending of the Catholic ENcyclopedia article rather interesting: the Albigensian "herecy was finally suppressed by ..." (I do not recall the year). No regrets even 800 years later. Thank G-d; it was menace; it was hard to get rid of; we finally did it.
The Albigensians believed that intentionally starving oneself to death and starving one's infant children to death were good things. They also believed that killing another person was an act of mercy, since physical reality reality was evil - that the world was created by the Devil instead of God. They were a death cult similar to the Solar Temple or Aum Shinryko.
The fact that Albigensianism stopped spreading was a very positive development for the human race.
You won't find the Catholic Encyclopedia saying that the Spanish Inquisition was a good thing just because it kept Spain Catholic. The Catholic Encyclopedia realizes that the Spanish Inquisition was an egregious example of the abuse of power, while the Albigensian example was a matter of civilization fighting for its life.
As for the factor of ten, try a factor of a thousand. There are people who will claim with a straight face that 100,000,000 people instead of 6,000 were executed by the Spanish Inquisition. That's right - people who claim that four times as many people as live in all of 21st century Spain were executed in Southern Spain in the 1500s.
The fact is that in the XVIth century the Dutch were engaged in a civil war against the Spanish throne. I'm sure that something like 50,000 people died over the course of this conflict. But separating purely religiously motivated executions from political assassinations and executions for treason is pretty much impossible. There was a Calvinist army fighting Catholic troops - every encounter would have some religious aspect to it.
If Fiske is going to chalk up the deaths of Protestants in Holland to pure religious bigotry, then he'll have to add all the Irish and Northern Scottish deaths and land clearances to England's and Protestantism's balance sheet. But he's already ruled that out - since he feels that the tender mercies of Cromwell in Ireland can't be compared to the brutality of the Spanish Throne in Holland.