You should be able to replace the new keyboard with the old. I did just that, although the circumstances are not exactly the same. A friend replaced her older iMac (it had the plastic keyboard) with a new one. The new one came with the aluminum wireless keyboard. I simply plugged in the old keyboard and mouse and she is having no problems whatsoever. FWIW, my Mac Pro (the original one, not your model) came with a plastic keyboard and it works just fine.
If you substitute the old keyboard, the firmware update will (most likely) not affect it. This is a guess; I can't test it.
Best of luck to you for a smooth, complete recovery.