It looks like Skylar has pulled herself together in order to keep the kids safe. She will do anything for Walt, regardless of how sick it makes her, including having sex with him, as long as he will leave he kids with her sister and Hank.
When Hank was holding the baby last night, I had a revelation. I think it's entirely possible that the show will end up with Hank and Sylar's sister raising those kids, because Walt and Skylar will be either on the run, in prison or dead. Very sad in deed.