Well first off let just tell you that all of that is not possible at
the moment, but there is some work arounds that might. Be able to
achieve what you are trying to do:
1. You can create subdomains with Google Apps and enable wave for each
subdomain so that way you can specify that users can comunicate with
others inside the network but not with anyone else.
2. Only if people add you as a participant of the wave, you will be
able to monitor the data... You coult make a New Wave extension so
that it will add you automatically but it will require users to use
that.
3. You can make a welcome page with the gadgets and extensions you
want users to use and make them install them prior to using wave. In
order. To monitor it's use you would have to be the owner of the
extension and have them hosted on App Engine.
Most of google wave is open source through: Wave Federation Protocol
www.waveprotocol.org so you can develop your wave client and monitor
it's own traffic and I think even customize it all you want on this
list. But in order to be able to add it to Google Apps you will have
to host it on App Engine (or at least have have an App Engine App that
redirects to where you have the custom wave client hosted) and add it
to Google Apps
Hope this ideas help! :)