To the games with good Inquisitor units I can add Disciples, and propably there are some other games out there with same stuff as well.
Zamolxis, I understand Your position, but You see, I'm sure that every kid interested in unit's names will find Inquisition Wiki entry and will be able to read as much as he likes of Loyola and other, khem, "brethren". Of course that this whole inqusition thing and witchhunt was an abominable part in our history, but the game is A Fantasy. Alternative world. Ok? So in this particular world inquisitors are not rotten pigs that prey on innocent, they are defenders of faith or whatever. There is plenty of fantasy books where good characters are bad and the other way around, not necessarily about good Nazi nations fighting evil Jews xPPPP.
Take a comic book "Spawn", where neither Heaven nor Hell gives a **** about our souls, all that counts to them is power. Etc, etc.
So basically, everything is possible in fantasy world, even You playing King's Bounty with Inqusitors and burning all oppossition in fiery death instead being a good boy, just for the sake of historal accuracy - Your game, Your call.
To me it would be a much bigger problem to see a Dragons that look like chickens, elves like refugees from a war zone and dwarves that are being a joke, i.e. "You don't toss a dwarf", which was the lamest part of Jackson's "art" I've ever seen
My opinion only.