The Arduino-compatible Teensy 2.0 and Teensy 2.0 ++ boards have native USB-MIDI. They show up as a class-compliant USB MIDI device and your OS will use it's built-in driver to talk to them. Also, MIDI over USB is faster (so, lower latency) than traditional current-loop DIN MIDI.
The comments about matrix scanning and diodes on your key matrix still apply. Probably useful to tread how a MIDI keyboard works and this DIYAudio forum posting.
So far, velocity sensitivity and channel aftertouch have not been mentioned - do your organ manuals have those?