The Inquisition

[Gothmog]

What you've described is exactly the situation Warhammer Fantasy Roleplay creates. Wizards are present and sanctioned by the state in the form of magical colleges, but rogue wizards, witches, and hedge magicians are hunted down mercilessly by witch hunters and the church of Sigmar. Wizards of the colleges are barely tolerated and not trusted, but seen as a necessary evil for the defense of the empire. The church of Sigmar will not suffer a witch to live, as the unlicensed practice of magic is consorting with the powers of Chaos, and can corrupt the magician, as well as the world and people around him. Even sanctioned wizards are subject to the power of Choas' lure. Its a very cool, dark setting, and it sounds like exactly the kind of thing you're looking for from what you said.

 

[Sidekick]

Warhammer RPG – that’s a good system, it’s got witch hunters, forces of chaos and so forth. Good gritty, dark medieval system. D&D can only go so far as a play system IMO. If you want to go the full hog then you should consider looking at other games as well as settings.

Happy gaming,
Sidekick

 

[Tharen the Damned]

Yeah, you can focus a Warhammer campaign around Witchhunters and their Victims.
There is even a Fluff only Book about Witchhunters and how to do it: Witch Hunters Handbook

Hail to Tzeench the Changer of Ways!

 

[Voadam]

Ptolus had an arcane witch hunt in its timeline with paladins burning wizards at the stake. I moved my Ptolus campaign towards reviving that scenario, and added some history to have it make more sense.

Demon pact making wizards, many who use misdirection spells to avoid detecting as evil is a good start. Have them be a major force in the wizards guild. The LG church/government finds out about it and takes steps to investigate. The wizards protest and refuse to submit to testing. Many wizards feel it is a politically motivated witch hunt and they are being set up as villains so they don't want to submit to testing. Some who get tested thought they could fake it and end up spectacularly killing their church testers when their evil is revealed. Hidden war starts with the demon pacters assaulting the church with summoned demons and the Guild denying it is their members doing it. The church responds with extreme prejudice against all arcane casters and gets arcane magic outlawed in general except under strict Church control. The wizards who refuse to submit are considered extremely dangerous threats and are burned before they can call in their demonic allies.