I think that possibly the pilot was paid to take the plane off course and fly in the vicinity of the island. He did not know there was going to be a crash. However, I think that Jacob knew the exact time of the hatch incident in which Desmond did not enter the numbers immediately. (just as the old lady knew Des was destined to turn the key at some point) He knew that the electro magnetic incident would pull that plane down.
That is why the pilot told them, "they will be looking for us in the wrong place" because they were completely off course (1000 miles off!). I always wondered how they got that far off course. But now I believe it was intentional. Then the pilot was conveniently killed before he could spill anymore beans.