If you disable protected mode you might see warnings like this when starting Internet Explorer Protected mode is turned off for the Internet and restricted sites zones or Protected mode is turned off for the Internet zone.
One way to disable or hide this warning is to set a registry value.
HKCUSoftwareMicrosoftInternetExplorerMainNoProtectedModeBanner set this to the dword value 1.
This will remove the warning.
This setting can be imported to the default user settings during your MDT or SCCM Task Sequence as explained in http://larslohmann.blogspot.dk/2013/03/customize-settings-for-all-new-users-on.html.