Having you tried overriding the global permissions on the individual Wiki pages? So you can restrict certain pages by user group rather than categories. Perhaps this is more direct that trying to group pages to categorize them. I still don't know if this would get around the problem of utilizing those pages in tocs and structures though.
I'm fairly confident that what you are suggesting can be done, it just a question of how to implement it. Give it a day or two, some of the more expert users are generally good about putting forth suggestions.