I think an ending where Makoto was left alone would've been just as conclusive. No one needed to die, though it's not bad that Makoto died, either - it was one of the two good choices they could've gone for in order to be consistent with the story; bittersweet ending for Makoto, or his death.
I still don't like Sekai's death though, I feel it was out of place. And I'm also a bit gutted mr. rapist got away scot free, but that's more a personal thing than anything.
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