I recall something about the children in ACC being more in tune with the planet because they were born more recently and still have a stronger connection people apparently tend to lose when their older. That seems to imply humans aren't all that different from Cetra and just need to put more effort into maintaining that connection and then figure out what to do with it. This would mean the main different between humans and Cetra are knowledge and culture. The city of the ancients looks like it was set up as more of a meeting place to do Cetra stuff as a group, what with the altar and that water projector, so it likely wasn't a permanent residence. Cetra settling and becoming humans before or after Jenova could go either way, though if humans split off from the Cetra before, one would think they would've been attacked by Jenova when it started going after other Cetra clans, as I doubt Jenova would've cared much who it was attacking.
If we're bringing religious references in the setting, I recommend looking up the gnostic concept of Sophia and how it relates to various personifications of wisdom, such as Minerva.
Is there evidence in the OG to suggest she was in an abusive relationship?
In the OG, Lucrecia's basically just there for expository purposes as Sephiroth's real mom and a tragic element of Vincent's backstory. We have her getting along with Vincent, then they have a falling out and suddenly she's with Hojo, letting him speak on her behalf without saying anything. It gives the impression that Hojo took advantage of what happened between her and Vincent to get her to go along with his experiment, seeing as she was completely quiet in the scene where Vincent was objecting to it. Her sudden involvement with Hojo after running away from Vincent is the kind of thing that can easily happen at the start of an abusive relationship, where the abusive individual takes advantage of the emotional vulnerability resulting from such things to get involved with the person, starting out by making them feel more comfortable around them and gradually isolating them from others or having them go along with their decisions more and more until they can pretty much do what they want. The DoC versions of the scenes are quite blatantly examples of stuff you could see in an emotionally abusive relationship, especially knowing how sociopathic Hojo is. Then, you have Hojo preventing Lucrecia from even holding her own child, which makes it pretty clear their relationship wasn't in any way healthy.
I have general misgivings about using the "she was in an abusive relationship" trope in fiction to excuse all the bad things a woman does. I feel that it denies them agency, almost like saying, "All women are nice and good really, so nice and good that they assume all men are nice and good, and then the bad men force them to do bad things." I would prefer her to be written as not being in an abusive relationship and freely choosing to experiment on her child, then belatedly coming to the realisation that she made a huge mistake of her own free will.
Fortunately the game also offers us Scarlet, who is clearly evil just because she likes it that way.
Just because it's an abusive relationship doesn't mean she didn't genuinely think experimenting on her unborn child would work out. Manipulations aside, Hojo still would've had to pitch the idea to her in a way that made it seem like any potential risks would be relatively minor and that she and the child would manage alright. Considering real life procedures that currently exist regarding genetically modifying embryos and how they may have even started with in vitro fertilization, making it seem like a safer procedure than it actually was should've been perfectly doable. There are plenty of genetically modified organisms out there that are perfectly healthy, including transgenic ones, which is when you insert DNA from another organism. We now have stuff like Goats whose milk contains spider silk, bio-luminescent cats, chirping mice and some plants that are more resilient than their unmodified counterparts. If the FF7 setting already had scientific research concerning the genetic modification of plants and animals through those methods, then a scientist who knew what they were doing should've been capable of doing that kind of thing to a human embryo just fine if moral debates were a non-issue. Jenova being what it is would obviously complicate things a great deal and cause some concerns but being the start of the Jenova project, they wouldn't have known that yet.
The main thing the abusive relationship does here is that Lucrecia would be more willing to listen to Hojo's judgement on the matter than Vincent's, as well as likely ignoring any doubts she has because she's not noticing the warning signs. It's like how people in abusive relationships tend to start out thinking things are fine and that all the friends/family telling them to break things off with the person they started seeing are just overacting or are trying to tell them what they can and can't do with their life. That's around the beginning of the abusive relationship, when the abusive person is still putting on airs of a good person you'd want to spend time with while getting the other person to distance themselves from all the people worried for their well-being, who, from an outside perspective, would be better able to see what's really going on. I'm not suggesting the abusive angle because I can't imagine a female character making the decisions Lucrecia made outside of one, but rather because the signs of an abusive relationship are already present and I feel that gets overlooked more often than not. If we were discussing a male character, I'd still be saying the same, so I'm not just trying to excuse her involvement in the Jenova Project based on gender. When this kind of thing is shown, especially in a realistic way, it's best to show it for what it is rather than pretend it isn't there. With how people tend to assume abuse is physical and overlook other forms, overlooking examples of those other forms certainly won't help people gain a better understanding of it.