I have a feeling that what happened in the season finally was not an event of reality. I would be willing to bet that they make it some sort of hallucination or dream
I don't think that'll be the case although it would be an easy out (Reshow that scene in the opener, then cut to House in the car shaking his head and driving away.) It'd be just as easy to deem the last season as part of his rehab in the clinic and he was just putting down his thoughts.
My guess is that it happened and she moved away for her safety.
What doesn't make sense is that the last two seasons she kept reiterating that the hospital wouldn't keep him around if it weren't for her yet now it seems the hospital is going to be keeping him without her?