Yes you need to keep the default mysql databases especially the 'mysql' database as that actually houses required information for the server. I would suggest a complete wipe and reinstall of your mysql. There are ways of restoring it but really it would be easier to simply wipe and reinstall it.
And yes you can create the databases manually and import just the relevant sql file data but the create_mysql.sql is I suppose for people who don't know how to create databases and more specifically users manually as the create_mysql.sql also creates a user account with access to that database specifically. I would highly recommend you not use your root mysql account for any databases on a real server.
