I dont know how your mill is wired at the moment but to me a spindle motor should be powered through contactors, there should be an eStop string that can disable the contactors so that nothing can operate the spindle if the eStop is hit. For your microswitch I would have this also in the line so that if the microswitch is open then the contactors cant operate. To do this would depend on how you have things wired but the way I would do it is on the operating circuit for the contactors I would have one relay for the eStop string and another for the microswitch string. These relays if opened would stop the contacters from closing and thus prevent your motor from operating but as each circuit is seperate the microswitch operating would not interfere with the E-Stop.
Hope this makes sense, it does in my head but sometimes my head is not a place others can see clearly in
Hood