Of course, she'll get her detective job back eventually. But once she does, assuming they remain a couple, I think they will try and keep the relationship under wraps for as long as possible, particularly for the sake of the hard-ass captain. She wouldn't look too kindly upon the relationship but then again, since Castle isn't a cop and as long as he is still helping to close cases, she might decide to let it slide. Or Castle can pull another, "friends with the mayor" trump card.
I think once they resolve the big "who killed Beckett's mother and why" mystery, they'll begin a story arch relating to the hinted-at mystery of the identity of Castle's father.