As I understand it, by the time they were into S2 they knew exactly what would happen all the way through. The only big diff has been actor changes; people leaving the show (for drinking? heh) or upgrading the role of Ben. It's not a huge change to the story though. All that changed was that Henry Gale was going to be offed in a few episodes, then in S3 when they're captured they would have been introduced to the leader of the Others played by a diff actor with the same character/backstory. They knew they were gonna be SF the entire time but they couldn't say that or the audience would dwindle from 23 million to 9 million, which is exactly what's happened this season. That's why they discover Adam and Eve in the cave at the beginning, as future proof that they knew what they were doing all along.