Not only is the ending a retread of Shadowbringers for the most part, they made it so we're essentially Emet Selch and then don't even bother to look at what we're doing. I do understand that a few of the Endless asked to be turned off, but it's not like we asked all of them. I'm sure you could've found a few people on the first who would've supported the rejoining too. What authority do a few casually picked "representatives" have to make that choice for everyone? This is also proof in and of itself they are sentient. They aren't just memories because they are cognizant of and can make existential choices.
Also, the argument of "they aren't alive, so it's fine" is literally the same argument Emet made towards us. It's obviously wrong there and there's a strong argument for it being wrong here too.
It is kind of bothersome that the game completely glossed over the fact that what we're doing could be morally dubious. I do get how they were trying to handwave it, but I just wasn't convinced. How many ancient civilizations does the WOL personally have to end before it's a problem with them?