Did you get any solution to this? I was looking for the same thing.
The scenario as I see it is this:
WP3 installed at http://example.com and this is where super admin creates and admins the sub-sites of:
I have no plans for users to be able to create their own blogs, just to have a network of independent blogs controlled by super admin at http://example.com
A user visits and wants to join or comment on http://site1.example.com and has no knowledge of, or care for, the main site http://example.com or any of the other sites http://site2.example.com or http://site3.example.com
However, as it currently works, the user is signed up to http://example.com and redirected to http://example.com from the sign-up and login process/emails and doesn't have any logical way to http://site1.example.com where they came from.
Ideally when they sign up to http://site1.example.com to add a comment or generally participate as a user, they are added as a subscriber to http://site1.example.com and redirected there after sign-up.
I guess it wouldn't be a great problem if they were signed up generally to http://example.com as a subscriber as long as I could automatically redirect them to http://site1.example.com and have this site recorded in their signup and welcome emails and they were redirected to http://site1.example.com after logging in.
That would also mean I could contact all users on the http://example.com network in case there was another site within the network they were interested in.
Anyone any ideas?