At i7MEDIA, we run a lot of mojoPortal sites, all separate installations for each client. Some clients have multiple sites inside one installation but clients never share the same installation.
We have, in the past, extracted one site from a multiple-site installation. It's possible and we can provide the service. I will say that if you are comfortable with SQL, it really isn't difficult, just time consuming.
As far as performance goes, it really depends on the equipment, traffic, and size of the sites. I can say that we have a good mix of small and medium sites running and they all do fine.
In our environment, upgrades aren't too bad really because we have scripts that we wrote to allow us to upgrade sites faster. We also install the sites in a manner that allows for easy upgrading. See this blog post for more information on that. We can share those scripts with you, if you like. You must be able to remote into the desktop of your server to use the scripts, though.