Why is Arrowood a villain? Almost everyone on earth has memories they would get rid of if they had the chance, even if it’s just the memory of something embarrassing they did that keeps making them cringe years later.
But plenty of people have far more serious memories they want to escape. It’s a cliché that a character drinks or uses drugs to forget. If in a movie we see a character drinking liquor and holding his head in his hands, we know with no dialogue that he’s trying to escape his past, or at least forget it.
What I’m trying to say is a project like this would have many, many happy volunteers and patrons. Someone working on a project like this would be seen as doing a great service to humanity.
Why does wanting healing make a person selfish? Is an amputee who gets a prosthetic limb selfish for wanting to be whole?
You can orient this around a moral statement that it’s irresponsible to run away from the past instead of seeking atonement and redemption (and really, this is a sentiment plenty of secular people share, as well as Christians—it was the message of The Lion King, for crying out loud!), but I don’t see any of that in your overview. It sounds to me like you decided Arrowood needed to be the villain and are now trying to figure out how to make him a bad person instead of just an antagonist.
As for Rubi: What’s the void in her life that she thinks restoring the memory will fix? In such a controlled environment, what happens that convinces her that her life is not what a life is supposed to be and that regaining her memory will fill that void?
You might want to make Rubi younger because YA protagonists are generally in their teens, but if she’s emotionally stunted from her lack of socialization and contact with humanity, you could make her act emotionally closer to a child despite being older.
If that were the case, could Rubi read a book of fairy tales (from some giant library Arrowood might have) in which there’s a story of a princess being captured and made to pretend to be a servant by a witch or something like that, which in her inability to parse reality makes her identify with the princess and want to escape back to where she’s sure she came from?
Could Rubi have asked Arrowood to erase her memories? I guess in a situation like this, you’d need to avoid a scenario where the entire plot could be solved by the characters sitting down and having an honest chat.
Could Arrowood keep removing Rubi’s memories when she becomes self-aware so she repeatedly thinks she’s a young child who has only been there for a couple years, but then she discovers old records of her over the years and realizes with horror that she’s actually an adult and that if she is caught out again everything that she currently is will be taken away from her again?
You could tie that into a character weakness of Arrowood in believing no person should ever have to experience pain, to the extent that he believes he’s doing the right thing by removing Rubi’s sense of self to prevent her from feeling emotional pain at her past and the way he’s betrayed her. He doesn’t even need a selfish desire at this point (outside of not wanting pain himself, which you could express through other ways like a drug addiction) but only a belief that it is okay for him to control the lives of others if it means doing what he thinks is best for them.
I hope this sparked ideas. You certainly have an interesting premise!
"...the one with whom he so sought to talk has already interceded for him." -The Master and Margarita