It's probably a metaphor insofar as we are aware, but it may well be literal. But it's a moot point.
Think of the ether; is there any real distinction between a ghost that's the amalgamation of ether with the mind, knowledge, appearance and personality of someone versus their actual spirit?
Regardless, we probably won't get a story arc with Tony's mind literally being freed. He has his problems; he's trying his best, still failing, but he can't escape them with a magical adventure. I imagine he will reconcile with Annie, but he isn't a character who exists to have his problems fixed.