the salient point is that it kills them out of self defense: they are conspiring against it and it knows. IMO it is not very terrifying in an existential sense.
I think it kills them not in self defence but to defend the goals of the mission, i.e. the goals it has been given. Hal forecasts these goals will be at risk if it gets shut down. Hal has been programmed that the mission is more important than the lives of the crew.
