This is a core function in wp-admin/includes/nav-menu.php. You can either hide the items with CSS or use the myEASYhider plugin here. IIRC, in order to actually override core functions, it must be done from a plugin rather than functions.php, so either way you’ll be using a plugin that could potentially be turned off by the end user. Perhaps it would be better (if not easier) to train the client on what these functions do and when they will or won’t be using them?
