Ben clearly spiked Smokey's kool-aid and let him loose, depending upon his knowledge of Smokey's programming, which likely can identify the most serious threat to the island, in this case posed by the group of mercenaries who were on the island less than a day and, literally or metaphorically, smelled of off-islanders, i.e. a threat. My guess is that Smokey's rampage in the woods the night of the plane crash was because it smelled a large group of new people, which indicated a threat to the island. However, he might be unable to approach within a certain distance of the ocean/beach, which is supported by the fact that we've never seem Smokey near/on the beach.
