I was thinking about this subject the other day when I tried to pull a pumpkin from Kakariko Town at night when no one around, but a message popped up saying something like, "You better not steal," or "Wait until morning to purchase" or something like that, point is I couldn't steal despite having a fantastic opportunity.
It made me a bit bummed out, for a Zelda title that seems to let us do anything we want, its a bit sad that one thing we could do in an earlier Zelda title (stealing) is specifically not allowed despite there being blatant opportunities within the game to do so.
They could still do the same thing as Link's Awakening to always remind you of the crappy thing you did, where everyone would start calling you Thief instead of Link. That way while you still get the item for free, you never live down what it is that you got away with. And yeah, the shopkeeper could still kill you again if he sees you again like Link's Awakening.