Hi
sunaboz and all!
For the continuation of my answer I quote myself first so everything is in one post now.

"I wanted to answer you with a post on this topic alone. I agree with you that I am curious as well where TD is aiming for with how Sophia was shown in the update. I do not think she is unhinged, remember what I theorised on black ops stuff? I postulate for now a personality imprint made on her to make sure she acts in certain situations without hesitating. We are talking about dark sh... from the secret services/black ops sphere.
I think her being groomed to be Abel´s successor is unmantling the work done on Sophia. For her to be a successful follow-up on Abel she needs to be herself and this will clash with and modify/erase whatever imprint(s) she received which do not fit her general personality. I think Abel is aware of this and let it run it´s course. It might be one reason the two doctors plopped into the club now. Abel knows that his unquestioning, unfailing right hand won´t be like this for all that much longer.
I am a bit sad that I misinterpreted Abel so far. I thought him being the well known humanitarian, he was working against the club knowing it needed getting the hands somewhat dirty considering the influence the club has. While it still could be the truth, Abel is also trying to win and profit over Chuck no matter what it takes. While it still is a noble goal seeing what Kath and Chuck´s brainchild, the VIP club, represents, it shows a darker Abel than we knew before. Still, if we want to bring down Kath and Chuck, we´ll need the help from van Doren too.
I too think that Sophia spoke the truth about hating Chuck, Abel and most of the VIP club members. Going by the fact that she remembers good times fondly and van Doren sometimes shows genuine fondness for Sophia, I theorise Abel rescued (and doted on) young Sophia from whatever place or situation she came from. Growing up with him and seeing the Good he did, she certainly came to some hero worship. She probably even volunteered to help bring down Chuck and his diabolical club, not knowing how far Abel would go to reach that goal.
Sophia certainly did not think it would be and come like this, with the special training she received and the mental work done on her.
I doubt the "glitch" in the club stairway was one, unlike some other times. Sophia went to apologise to Edwin on her own, without informing Abel. To cover it up, she played up something that Abel would have seen occationally, when Sophia and her imprints were at odds.
I theorise that the "Club bar, 'flat invader' Sophia" is closest to the core of her, an amoral, eccentric, calculating, nerdy genius. We see this in how she reacts to our laughing, when she is slightly despodent that her best joke failed and she now succeeded without even trying to. The talks our hero and she had, when she in a throwaway style hints towards some deeper things and events, like her thinking of herself as an effect/enabler. Now we know why, because to an extend this is the case.
The mental work and training done on Sophia ensure that she is capable of things she is not necessarily proud of. Kath most probably does not know about this, but her sadist´s instincts recognise the possible danger Sophia represents. It would not surprise me if Sophia got "Hitman" training.
On an intellectual, military level I see the logic, the cold calculus of war behind what Abel did to Sophia, to be and act in the lion´s den successfully until they take them down, needs both skills and mental fortitude to a degree which do not come by easy. And Kath, Chuck and their closest followers HAVE TO FALL no matter what.
But what was done to Sophia is abhorrent, even if meant for "the greater good". Because even if the imprints are removed afterwards, Sophia will keep her memories of what she and others did. In addition, part of the mental work will stay in cases it fits her core persona.
Abel and Sophia might succeed at taking down Kath and Chuck, doing the world a boon, but at what cost to themselves?