I agree to an extent that it would be far better to kill both of the brothers. I chose to leave them both alive only because of Clementine. Having a Daughter myself I think about the situation from a perspective of a father raising a child in a post-apocalyptic world. You keep your kids safe, show them what they need to know to survive and shield them from the darkness and depravity that desperation drives people to.
If I was by myself they would have been dead and I wouldn't have had any regrets, but I wouldn't want a child of mine seeing the would as a bleak place.