he didn't want to kill his clan it was an order that he had to follow....just because he did what he was told don't make him evil because he still had a good heart
he hated war and he didn't want to see anyone get hurt but his clan was about to start a war so by following orders he did what the leaf thought would be best...even while under the watchful eye of the akatsuki he still made sure his brother was ok never really doing any damage to the village when he was there because he was still loyal to them