Hello banh,
I regret to say that the limitation in such scheme is the common mode rejection ratio. Even with close tolerance resistors (and perfect temperature tracking between them) your op-amp inputs have to go from ground to the bus supply voltage at switching frequency. For a good difference amplifier such as INA117, the CMRR at 20kHz (a typical swiching freq.) is some 60 dB. I don't know the DC Bus voltage in your application, nor the maximum motor current, but I think that you'll see a high component of the switching frequency at the current sense amplifier output. I would not recommend to filter the switching noise because you could get a large delay to control motor current, for over-current protection for example.
Hope this helps.
Best regards.