I thought the widespread dislike was about how Naruto, despite having suffered immensely due to having been neglected in his childhood, neglects his own children for... paperwork

The author of this article seems to be the one misunderstanding something in one big way. Naruto incorporating science fiction elements doesn't make Kaguya any better as a character, nor does it redeem her awful introduction, and the main point of why she's widely hated is simply missed.