Without meaning to fan the flames of this argument any further, everyone seems to be overlooking the fact that both Chloe and Gwen were horrible people, working for a criminally xenophobic organization that was planning on vivisecting both the MC and pixie, and god knows how many they had already tortured before them. I can't feel bad for the scientist lady either, due to her openly admitting this without a hint of remorse or regret, in fact, she made it sound completely normal, like they was doing nothing wrong.
Not that the (some) fey are innocent in all of this no, otherwise the organization would probably not even exist, or at least would not be as extremist as it is, I mean, have you met Morgana/the council? However, given the choice between old and new Chloe/Gwen, I'll take the new ones. Personally, I don't see it as the MC having destroyed their lives, but rather, he gave them a chance at having new ones, which is, quite frankly, more than they deserve - in his situation, I would've just killed them both along with the rest for what they were doing.
Bear in mind however that this is just my personal opinion. We can argue about morality and what's "right" or "wrong" about this situation until the end of our natural lives that, unless we were all cloned at birth, we will always disagree on some portion of it.