I think you're missing my point. When you say:
>This is the only part where Tor mentions your killcount at all during the final cutscene, and that's more in reference to the fact that she attempted to blast her way to their leader and kill him to solve the problem
this is what I'm talking about. It makes no sense he tried to call you out on this because you pretty much had no logical recourse. Pacifism in the face of the genocide of your entire species is an unreasonable idea, so I can't count that as logical. This is why I wish there was some route where you could capture and reason with people instead of killing them. The new pacifistic aresenal is a step in the right direction, but I don't feel like it takes enough of that step to matter, because it remains a gameplay addition and doesnt affect the story at all.
You say Tor is a good leader, and I mostly agree, but I think some of the things going on are just retarded. It's been a while but I'm pretty sure I recall that you never really come to a good conclusion to the "you killed my friend" argument because Iji was right in killing Iosa off – her hands or otherwise. It's just reinforced with the new ending.
as for
>they begin talking about the concept of a handful of leaders not being able to fight against a mob of trillions, and why he was unsuccessful in stopping the war before it got to that point (which Iji accuses him of not doing, which is completely false)
I don't really see how this has much to do with what I'm talking about. Tor corrects her assumptions but she doesn't really care either way – it's a minor thing compared to the fact that it already happened anyway.
In the end Tor is still trying to guilt trip you for something completely justified, even if we take your argument into account that he only cares about the fact that Iosa is dead and not the rest of everyone. There are no mincing words here – she needed to die, one way or another.
The only way I can see Iosa not dying are if you never encounter her in the first place in a situation where you're on opposite sides, and that just straight up wouldn't happen unless you could do what I was talking about earlier – just say fuck it and ally yourself with one of the two factions, in this case being Komato in exchange for not finishing the job that the Tasen did or something like that.
My problem is that while I like that there are options, I don't feel like there are realisticly ENOUGH options. There are things that aren't being taken into account just because that would end up probably being a lot more work to implement than Dan Remar would want to bother with, though as he keeps making updates when he said he wouldnt this might still change eventually.
Tl;dr to my entire 3 posts could probably be summed up as
Again, redone because I fucked my spoilers up.