From what I understand, all of her "figuring things out" will actually be her basing her deductions on flawed premises. Her assumptions were wrong, hence all of her deductions that sprung from those false allegations are also wrong.
When you're so entwined with the "truth" that you've spent years entangling yourself in, years of "learning these things" about Nocton, it's going to be REALLY hard to change her mind about what's ACTUALLY going on.
Nocton hasn't been "horrible" at all. He's followed the morally acceptable rules that Duroa set for him as kids, despite not having those morals himself. Duroa is probably immune to an extent to the brainwashing, but Nocton doesn't know that. He thinks he MUST keep saying her last name because he assumes that their childhood friendship was a result of him initially brainwashing her. He wants to keep their childhood relationship because he feels that's the best he can get, so he doesn't address her as Duroa just to keep that brainwashing he thought was necessary to keep that.
Ugh I hope the misunderstandings get cleared up. It's frustrating, but at this point the misunderstandings have gone for so long and become so entrenched with further assumptions that I know it's going to take a LOT of intervention or time. We shall see.