Stopping the ship

In the goofs section for this movie, it is stated the no ship has ever been built or will ever be built without a manual emergency fuel cut of function.
I do not know that much about ships, but of course the crew should be able to stop the engines without using the computer and cut of fuel in case of fire.
However, in this movie doesn't the Scottish officer say, that they cannot get into the engine room because Geiger changed the acces codes to the doors.
If there are any sailors here, can you tell me, if modern ships have a way of manually shutting of the engines from the bridge, a way that no terrorist can mess with by tapping into the computer. I mean, you can most likely shut of the engines from the bridge, but is it electronically operated.
Do you have to go into the engine room to manually stop the engines.

What I am trying to say is, could they in the real world actually easily have stopped the ship, once Geiger jumped ship.
Is it true that there was no way of stopping the ship.