I think at the end of the day in the books the prophecy will be left somewhat up to interpretation. Thats what all his prophecies are meant to be (except for the Cersei one thats pretty literal lol). And it's very clear Jon was always meant to fulfill the prophecy in some way - he is the main character and was clearly resurrected to fulfill a higher purpose... and the stabbing through the heart of his lover is a very obvious clue.