What about in a sub domain? i.e. install Multisite in a subdomain.
Can I set up a subdomain that is something like multisite.example.com where WordPress will be installed and then which will create multisites such as site1.multisite.example.com or even multisite.example.com/site1?
Then have those multisite installations map to example.com/site1, example.com/site2 using the domain mapping plugin?