Be careful if you alter what happens with a throwing knife. One of the missions in the "Assassin" storyline requires you to kill a target sneakily using a throwing knife. He's not a trader, he's a military officer, so provided the reaction is only changed if you throw a knife at a trader, it shouldn't affect that mission.
Why does throwing a stone cost me reputation, but throwing a knife doesn't? This is consistent, I tried it several times, and against two different traders, saving game first so I could repeat the experiment and so that I was standing on the same spot for each throw. If anything, the knife ought to cost more reputation than the stone as it's a lethal attack - murder is a more serious offence than vandalism.
Why does throwing a stone cost me reputation, but throwing a knife doesn't? This is consistent, I tried it several times, and against two different traders, saving game first so I could repeat the experiment and so that I was standing on the same spot for each throw. If anything, the knife ought to cost more reputation than the stone as it's a lethal attack - murder is a more serious offence than vandalism.