After discussion with MySQL:
http://bugs.mysql.com/bug.php?id=29287

And with Debian, here's the result so far:

We don't like having cleartext passwords in files (regardless of the 
permissions of said file).
We want to be able to reset passwords etc. without a password if we're the user 
running mysqld.

Solution:
Patch (or wait until MySQL does it for us) mysqld to check who the connecting 
user is and grant full access if it matches the user it's currently running as.

-- 
Root password policy for mysql
https://bugs.launchpad.net/bugs/119075
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