I respectfully but emphatically disagree. The whole point of this is that you're doing what's necessary to save your world, and the souls of the living. Yes it's true that the ones you're erasing are little more than coded memories, but feeling so lifelike to the point that it even gives some of your friends closure...it's not supposed to be comfortable. Honestly, the fact that we know that Sphene's reality isn't sustainable makes it a grim mercy killing...imagine if it was sustainable, and you were essentially stopping genocide by committing it. We got off easy.

And like Elysium said, it's supposed to hurt. If you're not comfortable or conflicted, that means the story is doing its job.