Confirming the issue of not being able to get rid of indicator-messages apart from uninstalling it system-wide, but not agreeing with stuffing the menu with another item just for solving this. IMHO Indicator-messages should be de-/selectable in Startup Applications preferences (like indicator-multiload for instance is).

According to an answer on Ask Ubuntu [1], blacklisting all message-providers should hide indicator-messages altogether, but this doesn’t seem to work in 12.04, apparently because status-providers (which are different from message-providers) are still using the menu. (U1 Control Panel also seems to still occupy it despite being blacklisted.)

I’ve even tried overriding indicator-messages’ dbus service file with a hackish solution [2], but the envelope still insists on appearing (though without the associated menu).

* [1] http://askubuntu.com/a/15616/34756
* [2] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=544483#42