Do you really mean that, or do you mean the sketch in the AtMega 328P in the emonPi?
It it’s the former, how is your Arduino connected? If it’s via the serial port on the Pi and the FTDI header, the answer could well be to remove the outgoing data line from the Pi.
If it’s the latter, I don’t know - it’s a pain for me too, because I’m running the next test version, and that gets “backdated” to the stock one. @TrystanLea has made updating the front end sketch optional when it’s done manually, I don’t know about when the update is automatic following a power-down and restart.