Another idea is, when the user tries to write to protected folders, it
says something like :

"This(these) is(are)  system folder(s or files), and it(they) has(have)
been protected to ensure that your computer will operate safely. Do you
wish to write to this folder anyways ? "

[Cancel]
[Yes (field for administration password)]


Another option would be "do you wish to temporarily disable this protection ? " 
 - so the user can execute several operations on protected folders.

-- 
Nautilus should have a superuser mode
https://bugs.launchpad.net/bugs/12154
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