We've done something similiar at work. We've got an atmega8 with a xbee connected to the uart. The atmega8 is loaded with a bootloader (similiar to arduino bootloader) and we could program it from the a remote station (ie. pc connected to xbee module).
So, you should be able to connect a xbee to the rx/tx pins (with required level conversion circuit) of your arduino and program it from another one.