God damn it! I think he understood in the end. I hope he did, even if it was already too late. And the care he gave her all those times was NOT in vain. Marie treats Charles completely differently than any other person, especially from their family. It's sad to see them split like that.
Charles is easy to influence, so the change in his behavior was the main cause of friction, but he also misjudged his sister completely. He noticed how similar they were, in a way their family hated them both, but he explained it his own way. When Marie brought him the scissors, when she wanted to become an executioner, he thought her goal is the same, BECAUSE they were both hated.
He needed, wanted and imagine a soul alike his own in Marie and it was a mistake. So, when she gained power and started acting differently to what he imagined, he was terrified. Lashed out, freaked out a few times. He didn't understand the difference, didn't properly notice it, until it was too late.
A lot of story to go, whole Rogue to go, so maybe they can unite again. I hope so.