I'm sorry, life is brutal. Sometimes you need to kill, or be killed. And sometimes you need to decide, if getting your desired skillbok is worth stealing from some innocent people. Tough choices, this is what good RPGs are about.
The only tough choices I remember so far (having not finished even the first area) have been the fish thief and the two entertainers. But mostly stealing from NPCs is not a tough choice at all, because honestly, they just don't care. They don't eat, they don't use their money on anything, they don't do anything at all, they don't care if they made enough profit today to eat tomorrow and so on. They don't feel like people; they're just NPCs.
