Hmm, thinking loud without having looked at the things you can do in the c# libraries...
If there is full support to use the normal .Net-libraries in the scripts, how about setting up your own co-op web based gui? Do a simple aspx web site where you select maps, settings and assign players to different flights. Select formations or whatever and then save it all in a database. After all is set (add a simple chat gui) all players join the server and spawn at some random field. If the script can loop over all the currently connected players it can determine which one it should assign to which flight and "force" them all into the correct seat (based on database lookup of the configuration set in the web gui). After at least x percent of the players have joined (or a timer) it will start it all with all pilots in the correct plane, and in perfect formation...
Get my idea? The admin could even change parameters while the mission is running in the web gui if the script reads changed rows. A bit weird way of doing it for sure, but then we could do all we want (if the script can force a multi player gamer to switch plane). The admin can also go in and select "spawn 12 me 109:s at point x" while the mission is running. The web gui could also show an updated status for interested players that what to join.
We could even do a silverlight based real time radar operator map where a commander can issue orders etc
/mazex