Yes, but still, you can isolate the micro controller, USB, or what ever sensitive logic from the logic directly associated with the power part. This is exactly what i did for another project at work: I kept the motor, FETs and FET drivers on one supply, and all the sensitive logic and USB connection on another isolated supply. The signals coming from the MCU to the FET driver are opto-isolated. No any galvanic connection what so ever between MCU and Motor driver. If the motor generates tones of electrical noize, my circuit is still safe, not matter what.