Modern Empire policy sees Wizards as sort of like if the goose that laid golden eggs was actually a velociraptor. Working out a system where they lay their golden eggs in a place that is accessible to the Empire and turn their claws and fangs only against enemies of the Empire was an enormous coup that needs to be maintained, while trying to convert over to a factory farm system to maximize egg production is self-evidently insane. This is why the Colleges are allowed to emphasize and protect Wizard freedoms so much, because if the Empire starts trying to do that inexplicably widespread trope where you imprison and torture the dudes you give phenomenal cosmic power to and expect to fight your enemies, it becomes very, very easy to make them a better offer, and there are a number of beings, countries, and forces that are extremely willing to do so.
This is why Mathilde needed to be bargained with to get the Skaven stuff from her even though the other party outranked her, and why Vitae is not going to be snatched from her hands unless there's much better reason to do so than 'ooh shiny'.