I think you might be scoring at the end wrong. At least when I read my rules, it sounds like if the you don't score your Prophet during the game it only scores like a normal meeple at the end.
At least that is how I read
the rules wrote:
For each incomplete road and city, the player who has a follower on a road or followers/Prohpets in a city, earns one point for each road or city tile.
To me this does not say that the Prophet still scores double. So part of the key of the game is making sure your Prophet's city does get complete. You can't have an enourmous city that never gets complete and still get the points for it.