I don't know how Ben knows, but I don't have a problem believing he does know. Ben is a mysterious character, and his ultimate agenda is still unknown. He grew up on the island and has been there something like 30 years. There may only be a handful of people that know what is going on, but I'd bet he is one of them.

And you know that is not to say that he is all knowing. It seems obvious that he is trying to understand Locke's relationship with the island.

But back to the original topic. Maybe Ben thinks or knows that the group on the freighter are Dharma, and he thinks they will kill everyone in retaliation for the purge.

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Doctor playing golf. Woo, boy howdy, now I've heard everything. What's next, cop eating a donut?