Man, I am not one of those who says bullshit like Homura did nothing wrong.
But the thing is that despite what she did was bad it worked, all her friends/acquaintances are in a better position now, the Law of the Cycles is rendered obsolete since in this new reality there are no magical girls, and most importantly she keeps all the Incubators under a tight leash.
So yes, she is selfish, possessive and quite a jerkass, but she is far from being an evil monster.
Plus, just for this few seconds I forgive her of all her transgressions, Kybey lost and now him and all his fucking race are slaves to one of their previous victims, who tortures them daily.
Damm that ending was SO satisfactory!!!