Change the "crew insurrection" to "take over ship" or something like this. I can't see why a MC could not be converted to be loyal to another empire. How often you have the feeling your computer is not under your control?
He, a simple virus is much much easier to do and install then converting an entire crew of high professional personnel (remember, there are 100 or so ships that are crewed from a pool of billions!). And the "berserking" MC is showing that I make a valid point here. If this damn thing decides on his OWN! that isn't loyal anymore, why can't you make it loyal to yourself and not its former master?