You're right about the security issues with the blog. Basically the blog needs to be either fully open, or fully secured.
Have you already considered the idea of putting each knowledge base entry on its own page? That would give you ultimate flexibility since each page can be secured individually, and the menu/child page links would provide a nice organizational structure. You could even group similar topics within a page, and secure them at the module level. This structure would also be searchable and obey security settings if you're using the built-in search.
Other than that, I'd think the best solution would be a custom feature, but that would require quite a bit of work.