The placement of jin's flashback seemed to be in strange. My impression was it was a (hold onto your seats) a flashforeward/flashback. The importance of staying on course when leaving the island was stressed. Was Jin thrown from the freighter, either accidently or on purpose, while the freighter passed through the wormhole and returned to an earlier time. So while it is in the past, it is Jin's future.
This would leave him essentially dead to Sun and Hurley, the tombstone is a memorial, not neccesarily a grave.