Without being at a Mac now to confirm...
You could set the permissions for the MSIE preferences files (in the Library folder) so that the user does not control them.
Ideally, as an enterprise issue, you may look at something other than MSIE as Microsoft has discontinued development on it and security patches will probably not be coming. Try Safari or FireFox browsers.
- - I hope this helps - -
(Complain to someone else if it doesn't)