Well, this is a bit harder than we thought. Apparently the tests I did locally were on a brand new wordpress multisite database. You can not just add these lines to an older database because they have different tables.
define('WP_ALLOW_MULTISITE', true);
define( 'MULTISITE', true );
If you add these into an older MU config file you get a "Error establishing a database connection" on the front end and a "One or more database tables are unavailable. The database may need to be repaired." on the backend.
Repairing the tables does not help. I think that when you define multisite like this it is looking for some specific tables and structure that is defined in the multisite install.
I did a compare of the two table structures you can see here:
http://media.oasis.unc.edu/instructional_technology/compare-tables.png
So... I have two options right now I think (but please tell me if I am wrong). I can mess with the tables on the multisite install (27K tables), OR I can figure out a way to tell the plugin that this site is multisite without having those lines in the config file.
Could you tell me how I might accomplish the second option? It seems easier to modify the plugin than to start modifying the database. I hate to leave the dev path though of course so if you can add an option to the plugin that would be even better... :) I can't be the only one that had an old MU site and upgraded it to Multisite that are using the super cache plugin.
Thanks for your help Donncha!