Back in 2007 there was some work done to allow system admins to lock down GTK+ and Nautilus. File dialogs can only view white-listed directories.
This won't create permission problems for programs, but will simplify things for new users.
http://live.gnome.org/SummerOfCode2007/Reports/Sayamindu
However the code seems to be abandoned. Is there any other way to do this? Is there a similar project that still works?