I wonder what Eden was prior to the Quiet Rapture. Like, was it always a death cult, masquerading as normal? It was under Martian jurisdiction, and is pretty big. Cults like that don't usually hit mainstream consciousness without an active trigger event.
Personally I kind of see it being similar to Unitology in Dead Space;
(Keep in mind, part of Unitology's prayer is Through Convergence, we all become one. One mind, one being, one flesh. Hi, blood.)
it perhaps was initially a branch of New Age Christian faith before the Quiet Rapture and going fully off the cliff when the planets disappeared.
Simon's reluctance to let go of his Mom as a source of comfort despite her sending him to Eden makes me think the change in her may have been sudden, or possibly grief-fueled; he remembers his Mom as she was prior to him being shipped off, which is part of why he fights so hard.
(His Mom also gifts him the knife in what looks like a forest. I personally think the knife was not initially gifted for the purpose of killing humans, but rather for its designed intention-- skinning animals. We're 350 years post colonisation at that point, I'd say Mars has wildlife.)
Much of the doctrine we hear from the Father is very much post-QR (the Last Tree, there being no remaining soil, etc) so I do think Eden as it is in present times looks very different to the pre-QR Eden, though I do think it was still a cult.