So, that's an interesting point that I hadn't thought about. Locally
Integrated Menus (LIM) might solve your problems. Basically what they
are is taking a window's menus and putting them on the title bar of the
window in a drop down menu. Here's a writeup:
http://www.omgubuntu.co.uk/2012/02/ubuntu-12-04-to-ditch-global-menu/
That feature hasn't landed, but the specifics of the GSettings key is in
this branch:
http://bazaar.launchpad.net/~ted/indicator-appmenu/local-menus-single-menu/view/head:/data/com.canonical.indicator.appmenu.gschema.xml.in
So what you could do is turn on the LIM feature when VMWare Unity is
launched, and then turn it back to the user's setting when using the
normal desktop. I believe that (and I haven't used VMWare Unity so I
could very well be wrong here) you keep the window title bar, so the
user could get to the menus there.
Do you think that'd work?