Looks like we're heading for conflict between Toshiro and Yomiko. I think the fundamental difference between them is that he deeply empathizes with the transflorated while she doesn't. Even if her justification in this case is Ivy's crimes, it's probably a more general sentiment and a necessary result of having performed so many transflorations. She's also much more coldly pragmatic than him aside from that, being comfortable with sacrificing a life just to gain an advantage.
I'm really curious as to what the deal with Hikasa Ken is. Dr. Kudai seems to be set up to fill in that amoral, detached man of science role, unless there's a twist. But Ken is a bit of an enigma in his motivations, though we know he is pretty brutal based on the encounter with that politician. I'd really like to see Toshiro have some direct interaction with the anti-transfloration movement.
Given that the mass murder was largely accidental, I don't think Ivy can be blamed for that. The other murders were justified, if excessive. He targeted those involved with the practice of human furniture. Even Yomiko is at least complicit in that. Transfloration is ethically questionable even in the pure case of providing oxygen and deeply immoral otherwise. Those who are involved with it must bear some responsbility for this, all the more so given they live relatively lavishly within an impoverished society. And Ivy is mentally a child, incapable of finer judgments on such matters, given a gun and told to shoot at the bad men. Certainly there should be some consequences for him, but to be captured and tortured for the rest of his life is not commensurate to the crime.