Each document has a unique ID, and a document can also serve as the parent of other documents, thus forming a "tree", with a parent document acting as a "folder" for its children, and their children.
The menu generation code is passed a document ID to act as the root from which it generates the menu. I did much the same thing in a multilanguage site
http://www.bmptrans.ch.
The document whose ID is used as "root" for a menu generation script does not need to be visible. Thus, each of your separate sites would simply be stored "under" its own unpublished document, and the menu script would be passed the ID of its folder to use as its root. I suppose it would require some careful design thought to keep the document tree organized in the Manager, but certainly not difficult. If you have four separate sites, you could have four unpublished "folder" documents in the main root, (parent 0), and have each site’s content in its own folder. You can create a document group for each site, and assign the documents for that site to that group, and only allow the admin user for each site access to the pages on that group of documents.
The only issue I can see is the "site_start" default site entry document; perhaps have that be a single page with links to the other sites?