After contacting support their reply
Unfortunately Confluence does not sync the "disabled" flag from Active Directory, so it has no way of knowing that the user is disabled. There is an open feature request to have this added CONF-24786, so if you'd like to see this added, please add your vote to this issue, and feel free to add yourself as a watcher to keep updated on any progress. If this request was implemented, then any user disabled in AD would not receive the email, as they would be flagged inactive automatically in Confluence.
One workaround you could use, as mentioned in the request, is to add a check in the user filter for the disabled flag, which means users who are disabled will no longer sync to Confluence. For example you could use something like this to fetch every user who is not disabled:
(&(objectCategory=Person)(sAMAccountName=*)(!(userAccountControl:1.2.840.113556.1.4.803:=2)))
This workaround has the disadvantage that any history for that user in Confluence will be displayed either only by their username, or as "Anonymous".
An alternative workaround which would still preserve the user details in document history, is to add to the process that any users disabled in AD also have any groups which give them access to Confluence removed too. If a user is synchronised but is not a member of any groups with access, they should not receive this email.
I have used the workaround remove user from all groups in confluence.
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