The rabbit world is full of violence and the threat of death. Very few rabbits get to die peacefully in their beds with a bunch of grandkiddos gathered round, partly because rabbit carpentry hasn't advanced to making beds. Most rabbits in Watership Down face the constant peril of an icky death (or at least maiming), via getting poisoned or shot, attacked by farm animals (dogs and cats) or by wild animals (foxes and owls), or attacked by one's own fellow rabbits. But at the end of the day, it seems that this violence is the price that rabbits pay for living a free life out in the violent world.
Violence is a natural part of the world—it is neither good nor bad. Just messy.
Watership Down shows that violence is only proper when used to protect the weak from the strong. Cough Woundwort cough.