This is what David Shore says about that scene: "She’s confused. Is she jealous? I don’t know… There’s disappointment, even though I don’t think she was going to say yes… I love Shaun as much as she does, but you’re constantly trying to keep up with what’s going on in that head of his".
I think like most people there is a mix of emotions. While Shaun isn't her pet he is a constant in her chaotic life and the whole theme of the series is the positive effect that Shaun has on others. That constant has suddenly changed. I'm looking forward to the next series.