Ok, here is how I recovered.
I downloaded 0.8.9 to my computer, edited the PHP file to set $GLOBALS['wp-piwik_wpmu'] = true; and uploaded the files via FTP and directly overwrite the existing (upgraded) plugin files.
I then network deactivated and reactivated the plugin (not sure if that was necessary).
At that point, any blog which had received any traffic during the time that the new revision was installed was now reporting stats using a new site ID, leaving all the old stats behind. Any blogs that did not receive traffic resumed normal operations.
This now left me with what to do to restore the data for the 20 or so sites that were now operating on a new site ID.
I ran this SQL query in PHPMyAdmin to recombine the data:
idsite = "newsiteid" WHERE
idsite = "oldsiteid"
(Thanks to the good folks at HostGator for help with the SQL Syntax)
You must run that command for every single database table in your piwik install (NOT the WordPress database). That will move your stats over to the new site ID.
In the meantime, strongly recommending against upgrading to the latest version at this point.