It should be possible to write a destructor for a LocalStorage where the associated BaseRenderer is known.
I suggest to add a virtual method to the BaseLocalStorage:

virtual void DeleteStorage(mitk::BaseRenderer *renderer)

which is called for each Localstorage in the destructor of the LocalStorageHandler.
This is necessary for removing overlays from the overlaymanager and also to call ReleaseGraphicsResources on the actors.