The saved missions are in a file that is accessible to the user via iTunes. It is called flights.pList. The coordinates of the waypoints are all in there and the data can be turned into a KML file fairly readily.
Flights that are flown have log files that are accessed the same way. The data is a CSV file that can be plotted a lot of different ways. We are working to add support for it to our Log Viewer page: www.mapsmadeeasy.com/log_viewer
Offering a way to save the mission as a KML isn't a bad idea though... We will put that on the list.