For anyone who might be like me and couldn't figure this out because there was no option to delete a domain - let me save you 3hrs of playing - its because the user group superadmin appears to have that option turned off.
Goto Advance--> Group Manager, then click the PERMISSION word that matches superadmin (or whatever user you want). This takes you to the old fusionpbx permission module, then search for the heading Domains (not Domain Settings) and toggle on the setting called "domain_delete". Then save, logout and log back in and then you will be able to goto Advance --> Domain and find the garbage bin next to a domain.