Clearly a hall effect sensor suitable for DC current is what's required. The ideal unit will output 2.5 volts at 0amps rising to say 4 volts at +100amps and falling to 1 volt at -100amps.
An example of which is shown here http://www.hallsensors.de/CYHCS-C2S.pdf
These have total galvanic isolation between supply and output voltage so there are no problems with selecting a suitable reference point like you have with a shunt and they always produce a +ve output voltage so no problems of reverse polarity signals.