I think the game doesn't actually come down on the side that "endless aren't people." There are a lot of little moments that betray even characters who say that don't truly believe that. For example, Cahciua may say she is a false life and just a copy, but she also is the literal worst at hiding how happy she is that she got to see her little bun bun, how much she treasures that last little adventure she has, how much she cares that the other endless have a good exit. We, the player, also are sort of encouraged to see them as people, as we are told very explicitly to help any endless who can't move on to move on. We are told in no uncertain terms they still have moral weight, and that makes sense because our promise to remember them to ensure they aren't forgotten makes no sense if they are just machines.
"Is a human brain emulation a person" is a question for nerds. Its navel gazing. Its interesting to think about, but like so many fantastical questions, its not actually a good through-line for a story. It is better used as a vehicle to think about something actually relevant to the lived human experience.
If you look at Unlost World on that metaphorical level, it becomes clear what is happening: The endless are a society with no future. They are on life support. Their story cannot continue. They still matter, they are still people. But its the end of the line. You know what is happening. On some level they know what is happening, so many NPCs talk to you about how they are starting to come to terms with things ending if Sphene isn't successful. Or outright say they know what your doing and support you. So you treasure your last day with them... and pull the plug. It is a tragedy to agree that the cost of living is no longer worth it, but it not amoral to come to that choice, especially when someone is facing a natural end everyone faces that can only be extended by suffering.
Your WoL didn't commit genocide. They took a people off life support. In this case, the literal life of others.
It is SUPER not an accident that the final zone was a themepark for a themepark MMO. MMOs, Themeparks, summer vacations, they are inherently transient. Once a ride is demolished, once a server closed, heck once an MMOs system is gone... it will only exist in the memories of people who experienced it. Some day someone is going to walk into a server farm and delete the WoL and all the people you met and love in the game who are real to you, just like you did. Someone HAD to do that for 1.0.