Aside from the fact that a katana would probably be able to break the rapier, I also think that the iaijutsu would be a massive advantage against the fencing style. Assuming that the fencer knew about the iaijutsu, however, I still think the attack would be extremely effective, given the ease it can be changed to a two-step attack. While thrusts are indeed quite fast, I don't think they quite compare to the iaijutsu attack.