Is there are a way to restore System schema to it's original state?
There is no way to restore SYSTEM schema to the original state of empty database if you haven't backups, so you should recreate database. You could do this with Database Configuration Assistant (I'm using Windows Server 2012): run it, select delete database option, select database you want to delete, enter password to dba user and execute it.

After this you could recreate database with options you need.