From the FAQ:
After an attack is performed using Heavy Laser Cannon and all [critical hit] results are changed to [hit] results, the attack dice can be modified as normal. Any attack dice rerolled are not changed from [critical hit] results to [hit] results.
It doesn't explicitly mention merc co-pilot, but it does say you can modify dice as normal, which includes changing hits to crits. The example provided in the last sentence backs that up.