I may not be considering something essential here, but if the BT module communicates via UART and has a DTR output (like the USB interface on an Arduino), why not connect the BT to the in parallel to the USB interface (BT's DTR to the 328's reset circuitry, BT's RX and TX to pins Arduino's 1 and 0, respectively). Configure on your computer to have a virtual com port that works through the computer's BT radio, then upload from the IDE through BT instead of USB by selecting a different com port. From a (very) quick perusal of the Bluno wiki page, it seems they have the BT radio module replacing the UART to USB circuitry normally found on an UNO.
Is there something different about the BT module that you are wanting to use that I'm not aware of?