You are correct. Given what we've been told thus far, what the Alexandrians are doing with souls is sacrilegious, but not harmful. But people saw their favorite characters frowning and scowling and so they want to make them stop even though we were lectured for 40 hours about respecting other cultures. Obviously, killing people and stealing their souls is wrong, but there is nothing wrong with the voluntary system they have going in Everkeep, though I suspect they will add some way that it's dangerous so we can make them stop given all those frowns seem to extend to the writers' view of what's good and right.

As for how they'd have a stock of souls, most people die of disease and old age. Accidental deaths are actually the least likely way to die, so they'd have centuries of people who lived incredibly save lives inside Everkeep who never burned a soul. Sure you'd have fighters and hunters that burned through a bunch of them, but how often do you think the average merchant or accountant in Everkeep dies from an accident? They don't even have stairs for anyone to fall down.

Also, the lower birthrate doubtfully has anything to do with their soul usage as they seem to be the last living civilization on their shard, and the used souls go back into the aetherial sea at the death of the user, that's why the regulator is necessary to stamp their personality on top after they use a soul cell, cause that other person is still in them until death. The lower birthrate is likely due to the memory wipes. One of the number one reasons people have kids in modern times is to pass on their legacy. Legacy was a theme of this expansion, but the people of Alexandria can't do that because when they die their kids forget about them. So I'm sure many people wondered what the point of having kids would be if the kids wouldn't even be able to remember you after you died.