I think it'd be a good idea to change how the warning system works. Currently, when an option that throws up a warning is selected, the user reads the warning and must press OK. This results in the option being selected, and the user having to manually deselect it.
I think it should be made into an OK/CANCEL system, where if the user finds they may not want to select this option, they click Cancel which deselects it for them, since many users may not notice that the current system leaves the check mark in place.
Just a thought