Dawntrail's Final Zones destroy everything the story has built.

[Arzalis]

So no, I don't particularly feel it was an evil deed to shut it down. Because the cycle would not have ended any other way. The fact that we pulled the trigger rather than kicking it down to the next world to do it (hey, Refusal ending!), doesn't change the fact that it was unsustainable.

This is like saying "Everyone will die eventually, so murder is fine."

I do agree it was unsustainable, but it wasn't the individual people who were going around finding people to hunt down and live off of. They actually didn't do anything wrong. You can stop the system itself without directly ending the existence of everyone currently inside it. Maybe that leads to them eventually dying off, maybe another solution can be found. It doesn't matter now because we literally shut the door permanently.

I don't believe it's a hard concept to understand stopping Sphene from harming other worlds, but letting the Endless exist as they are. They're literally harmless without Sphene and/or the dimensional fusion device.