As discussed on the previous forums (the posts should be migrated over soon), I'm developing a multi-site plugin called Natom which will be released alongside AtomBB. Natom will have subplugins which depend on it like the Natom Hosting plugin, which will handle using Natom as a hosting platform and will allow you to do interesting things like suspending sites.

Natom will allow you to have the same sort of system on a per-site basis, while the sysadmins will be able a new rank which is able to manage the sites. The owner rank will be created as a "per-site" version of the founder flag (mainly insurance against lower level admins going after the main admin, although admins can do many dangerous things, so make sure that you can trust them either way) and will give the "owner" of a specific site immunity to lower ranking admins.

Natom will normally run before other plugins, although you should still mark your plugin via AtomBB's dependency system to make sure that there aren't any issues, if you're making a plugin that depends on Natom.
Natom itself will use different table prefixes depending on the site, although it will be possible to configure it to use multiple databases (be careful with this, as it may cause alot of overhead) and 90% of plugins should work perfectly fine with it.

I may be able to get an alpha of this out alongside Alpha 2, so you might be able to play with it.