#if ($context.currentUserEmail != $issue.fields.reporter.emailAddress) Your current template as is... #end
orit will ensure that the notification will render only when it is sent by non-reporter.
Or, alternatively, you can do the following:
#if ($context.currentUserEmail.endsWith("@yourdomainname.com")) Your current template as is... #end
The snippet above will check that the action was performed by a user with specific email domain name. It works, because, normally, your agents' emails are within one specific domain, while your customers are in other. Replace "yourdomainname.com" with a domain that is used by your organisation.