Though it doesn’t say it in the description the FeedBurner FeedSmith plug-in it does work on WordPress Network (Multisite) installations (WordPress 3.0X).
See here,
http://www.google.com/support/feedburner/bin/answer.py?answer=78483
for the details on the installation. Where it says “Activate” then instead just click “Network Activate” and the plugin will be available for all the sub-sites.
Within each site the Settings -> FeedBurner settings will be unique to that site.
What the plugin does is redirect the normal /feed path to the FeedBurner page that you have previously setup and have configured in the plug-in settings.