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It is obvious the Man in Black did it because of the way he reacted when Sawyer told him. As if he cares about a bunch of red shirts. He'd said to Richard that they needed to sort out the Ajira survivors. ("You know what I mean.") There are several times when the MiB's whereabouts are unknown, including before Ben calls the monster at Dharmaville, while MiB had Richard tied up in the tree, or before offering Ben a job in "Dr Linus".
- According to the "Lost Encyclopedia" published by DK, Charles Widmore's 'goons' killed the remaining survivors. (see page 14 under "a pawn in the war"). He did so to avoid interferences and witnesses.
- Lost Encyclopedia is chock full of mistakes. See here: http://lostpedia.wikia.com/wiki/Lost_Encyclopedia#Errors
- Zoe's presence among the bodies seems to support this.