Sensing DC motor current
While I understand that you are asking about how to use a current-sense resistor to sense current and then transfer the value over an isolation boundary, there are some alternatives to consider before you consider the decision finalized. 

(Note that you didn't give any specifications or requirements such as bandwidth, packaging, or current range, so the specific part(s) mentioned may not be suitable, but there is a wide range of parts available that will probably work fine.)

Hall effect current sensors allow isolated sensing of current without the need for any electronics or series resistors on the "hot" side of the circuit. The output can be selected to be suitable for direct connection to your isolated microcontroller. For example, if you had a 3.3V microcontroller, and the current you needed to sense was less than +/- 12.5A, Allegro Microsystems' ACS711 will give you a linear output voltage between 0 and 3.3V, with 0A current centered at 1.65V. 



To use this with your microcontroller, connect VIout to an ADC pin.

Of course, they make these sensors with different current sensitivities, capabilities, and packages. Digikey is your friend.