Well, before any more discussion develops, I would first like to ask a very important question; in the event that Sophia was a male and otherwise sexually unappealing to you, would your stance on her actions change? This should help determine whether or not your opinion on her soul-eating is actually based on the nature of her actions and not just her tits.
Secondly, I would like to note the use of real-world cases (using international law when possible but otherwise just following U.S federal laws) for ease of discussion.
For example, using the Nuremberg Trials of our own world as an established precedent, Superior defense ("I was just following orders") no longer absolves one of the crime and at most only lessens the punishment in question. Therefore, the legality of Sophia's soul consumption must be defended by an argument other than "she wasn't the one making the decisions," though even that should be called into question considering her position in the military and general power besides.
Finally, before someone goes and says "oh we shouldn't use our world's laws as a lens" or whatever, it should be noted that if we don't, the discussion quickly becomes pointless, as in-universe Sophia is apparently tolerated despite her actions during the war.
With all that established, it becomes important to determine whether we should argue Sophia's deserved fate from a legal or moral perspective.
It is considered unlawful to punish someone for actions that were legal when they did it but were made illegal after the fact (ex post facto). Depending on if soul-eating was legal or not during the war (I don't quite recall) Sophia's legal safety is in a grey area.
However, on moral and ethical grounds, we can assert that soul-killing is considered "evil" or otherwise seen as unjustified due to its currently unlawful nature and the fact that most people react with some degree of disgust or horror at the idea of it. Pedantic arguments against objective morality and society's ever-changing nature aside, it should be reasonable to state that the act of soul-killing is inherently a bad thing. Hopefully I don't need to explain the intricacies of why it is a bad thing.
Anyways, from there, it becomes important to determine just how bad it actually is--the moral weight of the crime. Is it worse than just plain old murder? I believe so, due to the fact that it robs the individual of the possibility of an afterlife or even reincarnation, which is presumably the natural state of things for this setting.
Whether or not it is simply "twice as bad" as murder or should be considered as "something even worse" isn't really important to us, as we can already assert that in itself, murder with purely malicious intent is considered heinous for obvious reasons. It's in bad faith to argue otherwise.
To some extent I suppose the powerup that soul-consumption provides could justify the act (depending on the situation), seeing as how being a high-ranking soldier in the middle of wartime necessitates certain actions to guarantee one's survival.
Even so, the sheer scale of her actions makes it so that she went far in excess of what can be theorized as "a justifiable amount of soul-consumption," assuming one thinks it can be justified at all. Parallels can be drawn to the use of excessive force in cases of self-defense, which is considered unlawful.
In that case, then, it would seem that even from a generous legal standpoint, Sophia's guilt is assured. Her innocence depends almost entirely upon whether or not the act of soul-consumption was approved of or even encouraged during the war, and from a moral standpoint, she cannot be found innocent at all. Irrespective of whether or not she makes my dick hard, I find it impossible to excuse her actions.
And that, officer, is why it is absolutely imperative I fuck her ass as hard as possible. Yes. It is for a good cause.