No don't drills holes in your cover it's too thin. I installed disc brake on my bike no problems. You need to get a threaded disc brake adapter.
you can get it from ebikes.ca This will screw to the cover on on the rear wheel. It's the same thread as the freewheel but on the opposite side of the motor. My 1000 watt rear wheel came with that threaded cover. Then a standard ISO disc will screw onto this adapter with 6 bolts. If you don,t have the threaded cover then your out of luck or maybe it can be ordered from GM. anyway it works fine.