I think I’ve answered this but I’m going to do it again. Yes, it does bother me. Although she was cleansed from Amon’s influence completely in WoL, I think there may still be a trace of evil inside her, perhaps not related to Amon, which explains why in the early missions she admits to herself “Jim was right, there’s something dark inside me”, while still in the human form.
Kerrigan is a controversial character. She went from wanting to dominate and conquer the entire Universe to facing her true enemies, while still aware of her past, what she did and the decisions she’s made.
I think Kerrigan could be split in three different ways:
“The good Kerrigan”
“The original, evil Queen of Blades which is gone at the end of WoL”
“The primal, cleansed Queen of Blades”
The primal Queen of Blades seems to be aware of who she is, regrets what she did in the past, and yet still wants the best for her Swarm and would go out of her way to make sacrifices. I don’t know her completely since I haven’t played LotV yet and so I don’t know what behaviour she will exhibit in LotV.
She decided to take revenge and in order to do so she went and obtained the primal Zerg form, which makes her more powerful than before. Perhaps if she never went to Zerus and if she never got the primal powers and remained human forever, she’d have eventually been killed perhaps by Arcturus and the fate of the entire Universe would be in the hands of the Xel’Naga. Remember the vision that Raynor was having back in WoL, if Kerrigan dies, it’s all over. And Zeratul knows that, and Raynor knows that. They’re probably the only ones who know that.
Regarding the civilian planets of innocent people, yes it does seem a bit odd since she spared a few innocent people on Char and the ones that Valerian was talking about. But when it comes to the Swarm, she’s making decisions in a way that would benefit the Swarm. And the essence collected on all those planets really helped with the evolution of her Swarm. One could conclude that she sacrificed those innocent civilians for the sake of the evolution of her Swarm. Selfish decision? Perhaps.
The story can be viewed from so many angles.