IIRC, Grimoire NieR (and/or some other supplemental materials, I can't remember) also strongly implies that Project Gestalt was considered a failure almost from the start, since Gestalt Nier refused to do his part in the final recombination process until Yonah was cured, and the people (androids?) running the project didn't want him to find out that there is no cure once a Gestalt has started to relapse. Even if Replicant Nier hadn't killed him, the Shadowlord would have doomed humanity anyway. You just turned almost-certain doom into absolutely-inevitable doom.
Well yeah, the Shadowlord was only delaying the inevitable, so it isn't a scenario with much hope for humanity either way.