is there any contraindication to use separate instances of puredata: one for audio file playback and the other for control/communication ?
There is no contraindication to do so and in fact many of my performance patches are two instances of Pd, one doing DSP the other one doing GUI and both communicating via Netsend/receive.
(the controling part would run as root - i could not get millers gpio object to work)
You might want to post the error descriptions and tell us about what did not work as well.