well no, the problem is still the directness of actions.
In the first case they are only acting on the trolley by diverting it, so they don't feel responsible for the death of the single victim.
In the second case they have to act on the person directly and kill the, so they feel responsible for it.
People feel responsible for their actions, not for their inactions.
What happens in the incursions is similar.
Destrying a world is a direct ation they take, while destroying the universe is something that happens on its own so they don't feel responsible for it even if they could have stopped it.
Of course brilliant scientists and magicians and leaders would be able to make the rational and responsible choice, the mess is the result of the writer's feelings.