I mean, let's just remember that Naegis plan to 'save' the remnants was complete personality re-write which included deleting not just the time spent in despair but also their first year at hopes peak, which for most was likely one of the best times of their life.Naegi's platitudes really do suck. I think it's supposed to be taken as the absolute furthest you can stretch the morally just hero's want to believe everyone is truly good deep down inside and can be saved. He tried to save JUNKO ffs, and she was disgusted he'd even try. Yeah Batman wants to help the Joker, Two-Face and Poison Ivy. But even Batman would have to reconsider if they killed millions upon millions and brought the world to the brink of ruin, but Makoto and Komaru don't and really, that's just stupid. What I'm surprised about is Kyoko and Byakuya were in agreement with him on it.
Like, he didn't just say "They might be good though", his plan was to literally brainwash them into being good people again. And you can't really say that he was just reverting them, because Komaeda, Fuyuhiko and arguably Peko were never good people.
Im not sure their ever talk about it, but what Neagi did was ethically disgusting.