I'm not 100% sure this will do what you want, but it's worth a try:
In the menu editor, for the menu item that you want to hide, use an HTML comment around the title for the menu item:
<!-- Title Here -->
I have an idea for some changes I can make to the framework which will allow for a better option, but it will take a little while to get the new code written and the patch updated, so this may be the best option for now.
As soon as I have enough time off from my other job, I'll start work on the menu update, as it's definitely something that needs to be done.