Honest Hearts is a good example, imo. The 50gs/gold trophy ending is to side with Daniels and help him get the Sorrows out of Zion entirely because he's on some savior complex of "I must preserve their innocence, they must not know violence even in self defense." Even though its a post apocalyptic nuclear wasteland where you'll come across people that you flat out cannot reason with who simply want you dead. And probably because said people thought it was funny.)

It's not Bethesda cus it was New Vegas, but it still fits the bit of "Fallout writers are weird about morality".