Just watched the series (am always late to everything) and while there are lots of things I enjoyed about it, and I can live with inconsistencies and plot holes and silliness, this aspect you mentioned is what bothered me morally about the series.
They establish that this little boy is struggling behaviourally/socially/emotionally/somehow, and the mother implies that mental illness like schizophrenia and neurodevelopmental disorder like autism have previously been considered and ruled out.
They then show how the little boy is repeatedly psychologically abused by his father, often in very nasty, insidious, manipulative, and plausibly deniable ways. God knows I'd struggle with how to look after and raise a kid with his difficulties, but the mother manages not to be abusive, and slipping into abuse is generally considered unacceptable no matter how challenging the kid.
If it were just showing an abusive father using the kid to get to the mum, or a struggling father pushed to breaking point, well, that stuff happens, so it happens in dramas. But after seeing all of the father's lack of care and nasty needling snideness towards Isaac (following the earlier total abandonment, with pretty-much-murder to come afterwards), we're then shown Gideon, the character who we've been led to believe is telling at least some version of the truth, explaining that the boy isn't meant to be here and doesn't have a soul. Gideon might not be totally trustworthy, but we see a lot of things that back up his story, so it seems he's telling something like the truth as he understands it.
To me that feels like it's pretty much angling for the viewer to think, "aha, so that explains it, the dad subconsciously knew something was off with this kid, something uncanny and wrong, which is why the dad was acting like that towards him".
I don't feel comfortable with a programme that seems like it's almost trying to justify a character's persistent psychological abuse of a child, that it's somehow reflecting an instinctive revulsion, perhaps therefore not entirely the dad's fault, maybe sending a message that child abuse could be understandable, that maybe doesn't really matter if the kid isn't normal, or could even be the right thing to do…
I also see uncomfortable parallels because autism was mentioned early on (seemingly as something that had been suspected but ruled out), and Isaac does have a couple of autistic-like behaviours. There's a famous quote about autistic children, "You have a person in the physical sense — they have hair, a nose and a mouth — but they are not people in the psychological sense," which was said by Ivar Lovaas, one of the scientists mainly responsible for the development of the popular/controversial autism therapy ABA. He said this in an interview where he explained and tried to justify the extreme and painful aversives that were used as part of ABA at that time on these non-person (soulless?) children. Autistic children have had some horrible stuff done to them and it was okay because they weren't really people, didn't really feel it like proper people would.
This series seems to be drawing on some deep-seated cultural ideas about the personhood of people who have behaviours like some of Isaac's, explicitly disavowing autism but sprinkling in a couple of stereotypical autistic-like traits to give him that authentic soulless vibe 😒
Even without the autism link, though, it felt to me like the series risked putting across quite a dodgy message in this respect. None of the characters said "It's okay to abuse children if there's something really not right about them" but it felt a little like the show was hinting at that, and I think some of the comments on this thread seem to indicate that I wasn't the only person to pick up on that message.