I just came from my dealer for software/firmware upgrade for brake. It is hard to describe but when I press brake pedal now I hear some noise. It is not a squeaking sound at all, rather it is like "sheek sheek" sound... Try to turn off your radio and slowly press your brake and check whether you hear same sound. I do not know whether it was there before recall since my radio was already on before...
Sorry but the noise you are hearing was probably there before and is something which is heard during normal operation of the hybrid system and its components. I can't see it turning up from them just reprogramming the ECU. I haven't heard a change with mine...
I can't tell any difference after the brake reflash. My brakes were great before and are still great.