When a witch controls the godfather, they then choose who mafia kills.
I think it should work the same way if the witch is controlling the mafioso. The mafioso is following the orders of the godfather - so if a witch is controlling the mafioso, the witch's orders should supersede the godfather's.
If the witch can cause a vigilante to shoot a mayor or even the vigilante's own self, then the witch's powers are strong enough to overcome the fear of disobeying the godfather.