Between Varun's modified Ardupilot code, and my modified LabView Ground Station code, there is now a complete setup available to those that have been looking for in-the-air waypoint updates.
Setup of the hardware from Varun's post: "The XBee's TX pin is hooked up to analog4 (one of the few pins we foundwas not in use) via NewSoftSerial and runs at 57600 baud. If it has a valid packet, it replaces the ArduPilot's next waypoint value with the one from the packet. After it hits this new waypoint, it loads the old next waypoint back in from EEPROM and continues on its original path."
Operation of the GCS is simple. With Google Earth already setup on a good view of the area, click 'Capture Point' on the GCS, then click somewhere on the Google Earth globe. The point's coordinates will be captured in the GCS, add an altitude, and click 'Send Waypoint'.
Since I don't own a Ardupilot (yet) I have not been able to test it. One person has successfully tested the complete setup, but please report any bugs you find.