it would be a good idea to isolate the AVR anyway.
Build a 5 volt supply relative to either side of the shunt. read the shunt voltage off the mid point between the two 500 ohm resistors, one to the 5 volt supply, one to the shunt.
The resistors will divide the 5 volts +/- the shunt voltage in half, the difference between the two should be half the shunt voltage.
This don't affect the resistors controlling the gain, provided they are a much higher value. say for instance a 100K ohm resistor from the output to a 2.5K ohm resistor feeding the negative pin on the opamp.
needless to say the tolerance of the resistors is crucial here, you may need a 10 turn pot to get a voltage of zero at no load.
i'm sure there is a better way to do this.