I think we do the same thing with a bit of a "cheat" procedure.  We have a couple of categories that we don't want to appear in the navigation.  So I hide the categories, generate the navigation, then go and unhide them again.  This way, they don't show up in the navigation, but if there is a button or link somewhere on the site, it will still go to the page without returning the error message.  Note:  The link will still show up on the main view categories page - we have made it go to the bottom so it's not mixed in with the rest of the categories.

The main trick with this method is to remember to hide the category before generating the navigation, and then remembering to unhide it after.

I'm proposing that the answer to your request is custom programming.

We, or one of the other developers should be able to do this in a few hours.  For a programmer familiar with the code this is a fairly easy mod.

When I said "add a flag to the category admin", I meant that literally.  We encounter the requirement you are describing frequently, and stock functionality fails to address it. 

So we add a flag to the category table, alter the category admin to support that flag, and then make alterations to the category page and category navigation generator that cause flagged categories to vanish.  That overcomes the issue you describe in your latest post.