I'd suggest not giving the wizard any reward for following the rules....
However, if you really don't have a problem with the spells, I might set up a situation where the council might make an exception.
It could be as simple as: There is a Rogue Wizard who has been casting contraband spells and the party is to track him down.  Due to the danger this wizard poses with his unregulated use of the Wish spell, the party is authorized to "any magical means necessary" in the removal of this threat.
Or it could be a longer-term relationship.  Example: The council brings in the Wizard and asks him/her to be their agent.  They are given a "License" to use contraband magic as long as they are working to further the council's ends.  Such a license would of course have to be up for periodic reviews, and that can lead to no end of fun as the players try to stay in the council’s good graces.
This moves the choice to the Player.... if they wish to use the spells, then they have to do what the council asks, if they are happy with how things are now...  Well then you have nothing to worry about.