Honestly, IMHO, she's already decided not to take the job and it's her thinking in hindsight about Senator Bracken that's allowed her to make that decision. She realizes that if she were to take the job, it would allow her to pursue him and she's probably worried that it's the only reason to take it and it takes her a bit to realize that and that it's the wrong reason. She realizes that she's in the job she's always wanted to really be in, the fact that Castle has asked her to marry him is just another thing to confuse her and cause a reaction.
Honestly, looking at all the available options, I don't see her taking the job being the way the writers can continue to do the show. If she tells Castle yes, what then, do they go to DC together? Does she go and Castle stay in New York? How could that work? Probably not very well either way. Things wouldn't be the same if they both go and Castle would find himself staying at home a lot when she's traveling the country. Obviously, it would be hard for the show to go on if Castle stayed in New York while she went to DC.
If she tells Castle no, then regardless of her decision about the job, how do you write the show? Generally when a man asks a woman to marry him and she says no, that ends the relationship. If she says maybe, or I need to think about it, well then, will we have to suffer through a year of heart rending grief on her part while she tries to decide? What about the job offer then? Not really working.
Sorry about the giant wall of text, but the main thing that bugs me about this episode is not the cliffhanger itself, but what it may lead to as far as writing the show. In years past, I really cared to know what happened, does Beckett die after being shot, what happens now that they've broken through and slept together, things like that. Now I'm more curious about how the writers get themselves out of this corner than I am on what happens to our brave heroes. That in itself is kinda sad.