The new HD version (in exavideo/exacore) supports the controller natively via input/evdev.cpp and input/shuttlepro.rb, but it doesn't use the SDL library for accessing input devices like the SD version. There's a good chance that SDL will recognize the controller as a joystick, though. This will make hacking something together relatively straightforward.
If you have the controller plugged in, starting sdl_gui may or may not produce a "No joystick found..." message in the console. If it doesn't (that is, it recognizes the controller as a joystick), you can probably start your hacking around line 1053 of sdl_gui.cpp. That code allows actions to be mapped to joystick buttons; there should also be some code in there for mapping seeking to a joystick axis.
If it doesn't recognize the controller as a joystick, you'll have to come up with a way of reading the controller events from /dev/input/event* directly; the input code in the exavideo repository could be a starting point for that.
-Andrew