While I’m not super-familiar with WordPress MU, you should be able to do what you’re after.
What you would do is:
Create a catch-all Sub-Server, by first creating a Sub-Server such as wpmu.example.com, then go into Server Configuration -> Website Options, and set “Website matches all sub-domains”.
Regarding the licensing – yeah, the Pro version is the Pro version, it doesn’t fall back to working as the GPL version if you exceed the license limit.