To be honest, I want to go into this menage a trois and start shaking some sense into some of these people.
Emma, for trusting this guy's word over her own instincts, and allowing herself to be a doormat. The sentence "He finally confessed he had some feelings for Carol so Emma's fears were not totally off base but it didn't matter since Emma lived there and Carol didn't want him." makes me want to scream. It basically means "I want someone else but they're not here and you are so you'll do". I've never met Emma but I guarantee that she is worth way, way more than that.
Carol for being rude when there's just no need to and for dragging out this drama further. How can you demand that someone not be in their own house at your convenience?
And lastly John for being a colossal jerk. Earlier I thought that this could just be a case of differing expectations which is no-one's fault, but "I want you...no, I don't...yes I do...actually I want HER but she isn't her and you're not a bad back up plan" is just inexcusable.
As for what Emma should do, she should be distantly polite to John until she can move out, she should say "I'm afraid that I can't accomodate that request" when asked to leave her OWN HOME, she should be cool and professional with Carol when she needs to work with her and never, ever speak of this matter with her again, and then she should get the heck out of Dodge as soon as possible and never, ever see or communicate with John again. Also she should stop by the store on the way home and buy herself a spine, or possibly some self respect.