And the Doctor is hers too. Without her, he would be dead, entombed on Trenzalore. She - with Gallifrey's help - broke that time line, and she is right: She is owed. She gave life, created the Doctor in her image, and then learned the hard way, over the past season, exactly who he has become because of this. And who she (the Doctor's mirror) has become as a consequence.
I think this is the much more interesting and bigger question of this season, and we got part of it at the beginning (what if the Doctor came back 'wrong'? He's come back from the dead, he's transgressed the normal bounds of Time Lords life, what does that mean? How does that change him?), but the corollary that you point out here only emerged over the course of the season: Clara has played god. What does that do to her? I hope we're coming back to all this next season, because the implications we see here with Missy are really grave.