I disagree. If a ship is designed with a master computer, then there is no crew and no bridge. Once the MC is gone there's no-one to convert and no way to fly the damn thing.
Maybe you should be allowed to put boarding parties aboard and then fly it home under reduced speed/ functionality, but using the AS makes no sense at all.
I would agree with you except for one point, a ship that has had it's MC destroyed can still fight.
Where's the logic in that? If MM would change that then the AS not working would be fine.