I think she's terrified because of how Season 4 ended breh.
You have Walt searching for his cash because he's about to get his family out of there and the fact that he was in real danger, then Walt basically tells Skylar he's responsible for what happened with Gus.
I don't think many women would just be able to shrug off that shyt like it's nothing. She's realizing she's dealing with a murderer... The last scene of this episode is just chilling because he's trying to comfort Skylar by saying, the hurting people, and the killing gets easier as it goes along
And then he just justifies it by saying, it's all worth it if it's for the better of the family. The real question is whether or not Hank feels the same way.