But it wasn't only that. The Church also promoted alms, charity, and asylum to those who asked for it. It was also one of the very few bastions of culture and learning remaining in medieval Europe. Not to mention the Inquisition and witch hunts is mostly a Rennaissance affair, not Middle Ages.
Point is, yes the Curch did some really nasty stuff, but that's hardly all they did. Dragon Age handles it much better, since it does show the zealotry and corruption in the Chantry, but also the better aspects as well, and has them opposed by factions that have their own moral baggage. That is gray morality.
With the Eternal Fire, literally the only aspect you see in TW3 are priests that are either cruel (Menge and his ilk), overzealous (most preachers in Novigrad) or fake/corrupt (the Fisstech dealing dude in Velen). The entire religion is a caricature of the Church's worst aspects. They are also opposed by Geralt the Good Guy and wizards that are entirely portrayed as poor helpless victims as well as crime lords with a heart. That is not gray morality, and not good writing/world building. Especially when the game takes special care to estalish an insane tyrant as the religion's chief patron.
I'm sorry, but calling the Catholic Church "one of the few bastions of culture and learning in Medieval Europe" is either sarcasm or not knowing history.
As it turns out, they had some of the best artists working for them (since they had the money)... But...
This is the institution that kept (through punishment of excommunication - if you were lucky, torture and death otherwise) the western civilizations from advancing from the ridiculous ideas of the universe, world, anatomy, sickness, geology, seismology, etc. that were the norm back then.
(Incidentally, inquisition belonged to the middle ages - starting in 12th century, while witch hunts started a bit later.)
The church - especially back then - had institutionalized hatred of anything not of their liking, bigotry, ignorance and a complete disrespect of women.
The few kind priests that helped people do not offset what the church's dogma and doctrines were, and how much pain and death they've brought to the human race over the centuries - through institutionalized dogmas and doctrines and politics, not as some indirect side effect.
Reading and owning the Bible in any language but Latin (once the flock were finally permitted to read the Bible, because for centuries, the Church only allowed the "flock" to listen to the priests, they weren't allowed to read for themselves) was punishable by burnings and (again) death.
Sir Thomas More was responsible for organizing thousands and thousands of burnings (murders) of english men and women who owned the Bible in English.
This is a historical fact. It is also highly likely he was torturing "heretics" in his own house (!) - which btw, he admitted to (keeping them imprisoned, saying he tortured only several... which makes it okay, I guess).
The same Thomas More was canonised in the 1930s as a martyr and declared the "heavenly patron of statesmen and politicians" in 2000 - long after everybody knew what a disgusting human being More actually was.
Please.
I have written essays on this, I could go on for hours and hours.
When I hear how the Catholic church was a bastion of knowledge, it makes me want to puke.
(even today, ask Africa how church's teachings that "AIDS is bad, but condoms are worse" is working out in Africa...)
My point is....
I have no intention in trying to delve into what the church in DA:I is trying to be or wants to be, etc.
TBH, I found the whole story and the world rather shallow and childish - for reasons I've described multiple times, from a cardboard world to no children in it, etc.
But CDPR is basing their Church of Eternal Fire on the Catholic Church of medieval Europe.
There is nothing gray about the Catholic Church of medieval ages. It was the world's most powerful organization (still is), based on ignorance and hatred, and brought about so much pain, death and misery that I'm honestly not sure why they'd be portrayed as anything other than evil.
(now this might sound harsh, but it just might be the best word to describe medieval religious institutions)