The switch example is more difficult to analyze in terms of the intuitions it evokes. I would guess that the principle of double effect captures an important aspect of what's going on, though I'm not sure how exactly. I don't claim to have anything close to a complete theory of human moral intuitions.

In any case, the fact that someone who flipped the switch appears much less (if at all) bad compared to someone who pushed the fat man does suggest strongly that there is some important game-theoretic issue involved, or otherwise we probably wouldn't have evolved such an intuition (either culturally or genetically). In my view, this should be the starting point for studying these problems, with humble recognition that we are still largely ignorant about how humans actually manage to cooperate and coordinate their actions, instead of naive scoffing at how supposedly innumerate and inconsistent our intuitions are.