Still sounds like if if you fix the usability issues, that you are left with an admin tool, something that users on a multi user system are subjected to, but that they cannot use (control)?
In other words, if user writes a new script and wants to test it out on some files, can he prevent any bugs in his script from deleting all the files in his home directory? Then, once he trusts the script, can he allow it to actually modify files in his home dir without requiring root privileges (remember, this is a multi user system, he is not root)?
Admins want to control what users do, they write security tools aimed at that. But what about users, how can I protect myself from myself without relying on an admin (or application packager) to have anticipated my personal use cases?