Last modified: 2011-03-18 13:03:41 UTC
In 1.17, disabled preferences aren't shown in Special:Preferences, but they do seem to be loaded and have their previously set values returned from User::getOption().
Are you saying that disabled preferences should be left in the database (unless the preference is ever re-enabled), but that User::getOption() should return the default value of the preference for all users if it's disabled? That should be fairly easy to implement...
Fixed in r84233.