Take the system administrator's access to everything, but put it through a read-only filter, and pass that to the backup program.
Instead of using the "File Open" dialog in the Win32 gui api... and then a "file open" which could go anywhere, replace it with a call to the file-open "powerbox", which hands a file back to the application. The user could even make it read only, append only, etc.
As far as users are concerned, it doesn't have to be hard. We just have to learn some new command line tricks.