How did you arrive at that conclusion? It seems to me that Nilfgaard grants conquered territories a good degree of autonomy. Places like Toussaint come to mind.
Radovid was pretty unhinged at the end of Wild Hunt. I'm not sure that I'd like to leave him in charge of Novigrad, burning heretics, witches, dwarves, and pretty much anyone that doesn't meet with his approval.
Autonomy? You mean control under a Nilfgaardian governing body, where Nilfgaardians get good treatment and everyone else is subjugated or killed, places like occupied Cintra and Aedirn come to mind, where innocent people were hunted down, butchered and taken as slaves.
Nilfgaard works very similarly to the Roman empire; it's great to live under... if you're
Roman Nilfgaardian or rich - But for the rest it's a resource-leeching, slave driving and cruel Empire which uses the masses of Northern bodies to install fear among the few that will remain if Nilfgaard were to win - It'd be easy to control the North if all the fighting men were dead and the survivors were put to work in mines...
I say Viva La libertà!
Also non-human hate is a thing which is widespread across the North.. It will only get more intense when the non-humans are blamed for the loss of the war and underground hate groups arise to seek revenge.
Mages plotted against the Kings, against one another and against the North.. Those involved in the plots are secretive and so a cleansing of a corrupt, plotting creed isn't uncalled for - But most of the mages would easily be able to get to Kovir, through magic or through evacuation.
The Witch Hunts last 4 years, 1272-1276.. 4 years of Hunts - An eternity in servitude to the Empire that will suck the North dry of it's identity and resources - No thank you.