Nah, I think she was realizing just how much her "team" contributes to her being able to solve the cases too. Ryan and Esposito both had significant contributions to the case that she might not have ever seen, and her and Castle reached the conclusion together, which is how they often do it. Then she did the whole, "You're in my interrogation room now" thing, which to me signified that she is in her element and this is what she's truly good at.
If she took the job in DC she'd be solving these cases on her own pretty much, or at best with whatever local people were available, and I think she was understanding that it wouldn't be as easy, or as fulfilling, or even as fun without the team she currently has around her. And of course without Castle. If he doesn't bring up the crazy alien body-snatcher-type theories, she often wouldn't get to the real answer. And of course she does love him.
So I think she was prepared to say she was turning down the job, they just played it in such a way that we thought Castle was going to dump her, and she was going to dump him. I think that the opposite is true. It might have depended on what he said and where he wanted the relationship to go, sure, but I think if he said the right thing that she was fully prepared to turn down the job.
That's my take on it anyway.
She might still say no, but she'll know he is serious at least.