Here is the process on how to delete an email from multiple mailboxes via Exchange PowerShell
Get-Mailbox -Database <DbName> | Export-Mailbox -SubjectKeywords “Subject” -DeleteContent
Make sure that the user who is running the command has FullAccess permission to the mailboxes.
In Exchange 2010 SP1 the command is:
Get-Mailbox -Server <ServerName> | Search-mailbox -SearchQuery ‘Subject:”subject here”‘ – DeleteContent