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Sayid had to be saved so that Jacob could prove that people can change/be redeemed. Flocke was so surprised (and not happy) to hear that "they were coming" because if they were, that meant that they changed the course of events and were not killed in the incident. This is very bad for MiB, because it means that free will is alive and kicking on the Island, despite the fact that he was able to find his loophole by "conning" the most ardent follower of Jacob into killing him.