First disable LDAP Authentication if not already done. Just uncheck the box and click save. Next under LDAP Directory, delete all the schedules configured. Finally you can disable the LDAP sync. You can also disable the Cisco DirSync service on the Publisher too. Then after a day or so, the system will note all End User accounts as inactive and another day later, it should auto purge them. All you'll have left are application users unless you add End Users after disabling LDAP.