Flynn, in my search to find a way to allow my WPMU users to be able to upload a new header image for their chosen theme (I've got over 100 themes available to them, but not all have a way to upload/change the header image), I found that somebody has come up with a nice way of doing it. You basically just have to add code to functions.php, which creates a new upload area/custom header option to just about any theme. Maybe you could incorporate this into ThemeFrame and even into Atahualpa, to make it easier to switch out the header image without using an FTP program.
http://wpmututorials.com/how-to/givi...ustom-headers/