If I understand you correctly...
You can stop just anyone from using this by requiring some form of authentication to use members_area_delete_account.php . If you have a session system in place, then you would check the session in here (I'm assuming this is the file you call from the browser, and function_delete_members.php is the scripty you're executing from the CLI).
To protect function_delete_members.php, move this script outside of your web directory. Or, if you don't have access to do that, make a "secret" folder on your webserver, and make a .htaccess file inside that folder that looks something like:
Order allow,deny
Deny from all