Hi there,
As Hyperic's community manager, thanks for trying out the new Zimbra plugin. You can certainly run the Hyperic HQ agent as root, but the old sysadmin adage about not wanting to do that should probably be adhered to. However, running as Zimbra user may well present other issues - such as the ability to access other application log files, for example. You might want to try a generic sysadmin user that has just enough access to everything you want to monitor.
As for future Zimbra product upgrades, do they wipe out any manual configuration that you do? Let us know if you need us to lobby anyone
-John Mark
Hyperic Community Manager