Agreed. Emma could have very easily shot down Neal or declared that she had stopped loving him and boom. Done. But no, the episodes repeat the same theme: they still love each other and always will.
If they wanted to put a nail in the SF coffin they could have actually had her secret have been the kiss, and that she had feelings for Hook. But they didn’t. Instead they had her secret be about the conflict she feels over loving Neal, which quite clearly showed that she and Hook are not on the same page in regards to what that kiss meant.
This is why I think the CS hook-up had to happen in NL, when Emma’s inhibitions are lowered and her emotions are all over the place. I think NL was like a week at Vegas, and even after 3×7 you could tell Emma was regretful about leading Hook on. What seemed like something more was really just a kiss to Emma. I think she regrets ever kissing him because it has only served as a major distraction from the mission of saving Henry.
Don’t remember where I saw this comment, was somewhere on tumblr, but someone said that maybe the reason she’s suddenly wearing a turtleneck in the next ep is because she’s actively trying to cover up the goods in response to Hook’s advances and she doesn’t want him getting any more ideas and doesn’t want the distraction of him being distracted any more. Of course, it could also just be that it gets chilly, or that they wanted her wearing black for aesthetic purposes for the scene with Regina, or it may even be to symbolise her joining forces with dark magic again. But it is a pretty drastic costume change to go from tank top with lots of bare skin, to a turtleneck.