I think she knew he might have it in him to attack her again, which is why she stays far away -- opens with her pregnancy, even -- and I don't think it changes either of them -- or their relationship, or what he did -- but her motives were the same in both cases: To save him, without sacrificing herself. To show him kindness and respect that he doesn't deserve, in the name of their history and how much she loved and loves him, even while her story is continuing, and his has stopped.
"Rolling In The Deep" is such an everywhere song that maybe the words don't mean anything anymore, but I always thought the saddest thing about it, at the bar mitzvah, was how literal it was: "The scars of your love remind me of us/ They keep me thinking that we almost had it all... I can't help feeling we could have had it all." And you have the obvious "scar" there, but then too there was that Chinatown thing where the scar on her cheek was this sign of something truly terrible inside of her that she kept trying to hide, became part of Sophie's judgment of her without ever knowing where it came from or what it meant...
I just feel like the respect she has shown him, before the window to right now, is one of the best things about her, because it's entirely about her. Compassion isn't something you can ask for, or demand: It's for us to give. It's a gift that we're able to give it. And I think that's so much stronger than the other ways she tries or might try to stay away from the stuff that could damage her, or the sternly Blair ways she does most things. Compassion isn't about what Chuck deserves, because he doesn't deserve it, because it's not something you can deserve. It's something that arises out of you, and represents your negotiation with the difficulties of life. The depth of your own spirit.
Maybe that got a little lost in the awfulness of the window thing -- not that she walked into that tiger cage entirely expecting and accepting what might happen and determined to go through with it anyway, because I think she was as shocked as we were, although it's not entirely off-base either -- but to see that scene brought back around here, with her displaying the same level of concern and compassion as before, it says wonderful things about her.