I remember that the Order of the Flaming Rose erected some sort of barrier that greatly suppressed magic in Loc Muinne, something similar could be used in Novigrad. But there aren't that many mages to begin with, and many like Felicia who you see at stake are novices.
Exactly. Most of those burned at stakes are novices. Margarita Luax-Antille says, that (at least after I imported save where Mage Council was established), that witch hunters slaughtered entire Aretuza (school of sorceresses), while Council and Conclave allowed it and even helped Radovid in it, after he gave them political positions at his side.
And Witch Hunters are not exactly weak mooks - they are (at least some of them are) a fighting elite, that Radovid trusts enough to use them as personal bodyguards. They are trained in fighting mages, and often use dwimeritium to supress their abilities.
And not all mages can teleport - it's safe to assume that novices are not powerful enough to do that, and even powerful sorceresses are able to teleport a maximum of themselves+1.
Besides that, just as in Dragon Age (perhaps far more so), not all mages are trained in combat. In fact, most of them are not. Your average mage has never even fought in his life.
They are mostly unwanted children of rich parents, who had a life of luxury and splendor, with everyone dancing to their whims. And suddenly, there are trained people with swords all around them, kicking them in the face and putting dwimeritium handcuffs on their wrists.
I WANT TO BELIEVE!
I'm still hoping they will do an expansion in Dol Blathanna. It was supposed to originally be included in The Witcher 2, but they didn't have time and budget and it was cut out from the game (Act III was supposed to happen there). Game is doing great financially, so maybe we'll get more than those 2 expansions.