At a practical level, there's another significant difference between the two cases: confidence in the probabilities.

As has been pointed out above, the thought experiment with the donors has a lot of utilitarian implications that are farther out than just the lives of the five people in the doctor's room. Changing the behavior of doctors will change the behavior of others, since they will anticipate different things happening when they interact with doctors.

On the other hand, we haven't got much basis for predicting how choosing one of the two scenarios will influence the aliens, or even thinking that they'll come back.