Sensing voltage with respect to virtual ground
Having the gnd of the MCU at the same potential as the -ve rail of the op-amp is not a problem in principle.  However, with respect to gnd Vsense(max) is at +0.5V. GNDREF is at +6V, so the effective +input of U?B is -5.5V. Therefore the op-amp output will saturate negatively and output 0V over your full sense range.

You could just use a single supply op-amp circuit to drive the MCU (ADC?) input.