If zimbra cannot do it you could export a list of username/password (not sure if this is possible) and then patch together some external script to delete the emails via some imap-tools. (I would go for a perl-imap-module)
Another thing is that zmmailbox has a deletemessage and a deletefolder command. So this might be a much more practicable and efficient way to go for. Use zmprov to create a list of users and then with zmprov/zmmailbox create a list of folders per user and then apply the delete-commands.
for a starter
hope this helps,
Release 7.1.3_GA_3346.UBUNTU10_64 UBUNTU10_64 FOSS edition