Here, she just found out she's the daughter of a crazy bitch determined to rule the world (or something like that) who ripped her heart out to prove it, and that she is infused with Life Fibers that does horrific things when it goes out of control. It might've reminded her of her transformation, and she put two-and-two together while she was having her fever dreams (I think that's what they are). I actually think she's trying to protect Senketsu here. Ryuko must know both she and Senketsu are in danger, and she doesn't want him nor anyone else to get caught up in it. If Ryuko hadn't grown as a person, I don't think anyone would be on her mind except herself and her desire for revenge. The revenge plot has been part of the background for a while now, she's thought less and less about avenging her father. Even after this episode, I don't think that's her main goal right now.
At least that's what I think is happening. I honestly doubt she would 100% reject Senketsu after all that has happened between them. Doesn't make it any less heartbreaking, though.
I don't think I explained it right... my mind's still reeling right now to form sentences that make complete sense while backing up what I'm saying.