the D&D movie included a wizard's cabal within Thonia. They seemed to be the ineffective ruling council of the empire...
Interesting. The Empire from the movie was called Izmer/Izmir. Although Arneson did suggest it could exist on the same world as Blackmoor ("Beyond the great mountains") I assumed it was a different country than Thonia?
My thought is that it is specifically located within Blackmoor.
The Cabal was founded in the North as a way to end to the Mage Wars. This was all connected to the magical energies found in this particular region.
It occurs to me that the Wizards Cabal may have had a greater influence in other parts of the Empire before Uther's rebellion. While I doubt they were ever in a position like the one they currently hold in Blackmoor, Ursula Zov's accord with Uther may have caused the Cabal to become shut completely out of the Empire.
This is a price the Cabal may have been more than willing to pay, as their primary interests are in this part of the world, not the empire.
I suspect that Wizards in the Empire are instead forced to serve the Throne. Sorcerers are hunted down as in the North, but this is done by Wizards who are loyal to the Emperor, perhaps with the help of Clerics and Imperial soldiers/Inquisitors.
The Scoll and Blade may be one of the few arcane organizations able to operate both within Blackmoor and Thonia.