Well, I would think that something like that could easily be overcome by making the application menu easily able to be restored from the desktop. IE, treat it like a widget that can be turned on and off from the main menu just like you can turn other desktop apps on and off. Since the main menu will always be there, it would be a fallback option.

Seriously, if the lack of ability in removing the apps menu is to protect newbies, then just add another out for them in another area. It's not rocket science. I've done that plenty of times when designing similar systems for other UI's. It's sometimes referred to as the "life preserver principle". IE, allow them to sink their boat if they really want to, but always have that life preserver nearby so they can keep from drowning.