Yes, you are mostly correct. A ghost in this instance is more an old memory or person - e.g. an ex boyfriend as heart is used to indicate a romantic / emotionally matter. You could rephrase it as: 'She's still upset over the thought of you'. Remember that most lyrics in songs are very vague and quite often so abstract that they have no real meaning. They are also frequently grammatically incorrect as it is more important that they sound good!