It is possible to customize the outer email template that is used as a wrapper for all emails that are sent from Discourse. Doing this allows you to add branding to emails that are sent from your site. Details about how to do it are here: Customize and style the Discourse outer email template.
If you use this approach, you will probably want to disable the apply custom styles to digest site setting so that summary emails sent from your site will not have your branding displayed twice.