I think you'd have to play up the anti-Witcher sentiment to give the Witchers a downside, but that also wouldn't jive so much with a world where the training and creation of Witchers has revitalized.
I do like the idea of lower-power Witchers as a compromise. Maybe set it up so that somewhere in the timeframe, the Witcher Schools became specialized, so you'd have one specialized in combat/physical augmentation, one specialized in Signs, and one specialized in Alchemy. Not that the others wouldn't have some of it, but only the specialized schools would have the full breadth of their specialty, and so Witchers would now operate in groups of three. Or something. More like "Special Ops Teams" rather than "One Man Armies."
Though if full-blown Sorceresses are allowed, full Witchers probably could be too.
Or conversely get rid of Witchers altogether, but some small fragments of them have survived, leading to lesser-powered replacement monster-hunters of a less mutated bent. Could do something similar with Sorceresses.
Either way, it's certainly a setting rife for exploration.