Napoleon, in an attempt to maitain control of his farm in its weakened condition, has elevated his tyranny to extreme levels. He violates the commandment "no animal shall kill another animal" by having the hens and the other "troublesome" animals gathered up and attacked. He is trying to strike fear into the hearts of his "people" in order to keep them loyal. However, like most tyrants, his immediate success will be followed by eventual downfall.
After the deaths, the commandment is changed to "no animal shall kill another animal without reason". In this changing of commandments, the last commandment is also being violated "all animals are equal". Clearly, they have not been equal for some time.