With regards to hybrid configurations - we disable the on-prem AD account as well as removing licenses in O365 and converting to a shared mailbox. To "delete" the user, we move the disabled AD account to an OU that is outside of sync scope for Azure AD Connect. This has basically the same effect as deleting the user in Azure AD.
I will say we don't do any of this manually. We have a PowerShell script our Service Desk staff runs that basically does it all. (We also change a lot more than what's listed in this article, such as automatically setting an Autoreply message, disabling ActiveSync, resetting the password, removing their picture, hiding the user from Address Books, removing the user from distribution and Modern groups, etc., etc.)