Why do you need the complex isolation in the first place, wouldn't it be easier to put the µC/ADC on the non-isolated side and isolate the digital signals (or debug interface) instead, it is really much easier (and considerably cheaper) than trying to isolate the fragile and easily spoiled analog signals? Isolation makes sense for user safety, not for circuit protection. Furthermore, isolated is not really isolated at AC, it still has shunt capacitance across the isolation gap, which sometimes causes a great pain and agony for the system designer. Thus it is best to not have fast switching transients across the isolation.
Even the phase currents can be measured against the non-isolated ground (by putting sense resistors between HV ground and bridge switch), when sampling of it is timed exactly when lower switch in the bridge conducts (An usual feature of motor controller oriented DSCs).
I believe many motor drives are done in this way. You can get isolated debugging interfaces, at least for TI's C2000 series of digital signal controllers.
Regards,
Janne