There's a difference between
intent to portray something as negative, from an author's perspective, versus the
execution of that portrayal and whether it actually aligns with the manifested details within the writing. There is actually no question that the writers were hoping/anticipating we'd be disturbed by aspects of the Ancient society. We weren't, and many of us, for many reasons described, found the methods they used to achieve that either ineffective, unconvincing, or actually doing the opposite in making their society
more appealing. So I feel like people are sort of having two different arguments here.
In that long Famitsu interview, there's a bit that wasn't translated directly where Yoshida actually goes into how he thought players would leave Elpis thinking the Ancient society was "scary" - listing all the reasons he figured they'd be a little disturbing - but that instead, most people came away with thinking they were just "good people" instead.
EDIT: Here's the relevant part of the interview, if anyone whose Japanese is better than mine wants to correct me:
