Those souls finally "won" their body and Berath wants to put them on the waiting list again. Who knows when they will get another body again?! Just look at how many creatures (mostly kith, and wilderers) have been killed either by your party, rioters, undead, self righteous idiots or by Thaos and co. All those creatures won't be fathers and mothers anymore. Think of how long those souls would have to wait with such a decrease in population and therefore lack of reproduction. This is wrong both economically (I consider souls and bodies goods to make it simple) and morally which leads me to the conclusion that Berath is total moron and can't even do his job right. Technically he should support Hylea, because that's how they will get back to the cycle properly.
1. The events of Dyrwood are a small part of what's going on in the world. There are plenty of babies still being made elsewhere.
2. Even if they did have to wait a while, so what? Is their soul going to get bored, while it sits in the ether? There's no evidence that souls have any form of consciousness when they leave the world and return to the cycle.
3. Putting souls back into the bodies would be even worse. They would AT BEST be children with the minds of newborn infants and AT WORST be children with memories of being chained for years along with hundreds of other lost souls. Putting them into the cycle allows them to be born again as healthy, normal children with no memory of what happened.
1. There's also plenty of war being made elsewhere. People are savages and have a low lifespan, even elves. Even if someone was immortal, that wouldn't mean they'd be invulnerable. Most die before reaching old age.
2. Your main char is a watcher and you are telling me souls do not have a consciousness? At the end you are literally talking to a soul imprisoned in a huge adra pillar and you are telling me they have no consciousness? Souls are being ordered to help you descend into a huge pit. Not only consciousness, but that looks to me that they even have some kind of ghostly body on top of that.
3. Far from worse, but I agree that this isn't the best solution either. Their trauma will be forever remembered whether you put them back where they belong or let them rot in the ether for maybe a few seconds, maybe an eternity until they find a new body. Those people in Noonfrost trying to get to Rymrgand's domain... you should hear them out for once. They are sick and tired of the cycle.