Well, it could have been a valid question a few seasons ago if one of the others just popped out of the woods as if by magic...OH SNAP!! IT DID!! Remember when Harper just appeared in the woods in S4E6 (The Other Woman)?? Now that was a genuine mystery. She's not there, whisperwhisperwhisper, she's there, whisperwhisperwhisper, she's not there. I would STILL like to know how that happened. Richard, not so much.
I'm pretty sure that in this scene, Harper was the MIB. After whispers, she appears out of nowhere to deliver a message (allegedly from Ben) that Juliet is supposed to stop Charlotte and Daniel from completing their mission at the Tempest. Harper said that the folks on the freighter were planning to kill everyone in the island with the nerve gas. Funny thing about this situation is that during the time that Harper was supposedly under Ben's orders, Ben was being imprisoned by Locke downstairs in the Barracks in the same room in which Locke's father was previously constrained. This is the same time that Miles asks for the $3.2 million.
That is possible that Harper was the MIB, but I never associated the whispers with the smoke monster. Especially after the episode where we see Ben kidnap Alex. He tells her that if she wants to live, whenever she hears whispers in the jungle, to run the other way. That tells me they are directly associated with the Others because you can't really make a threat on someone else's behalf, because as we have seen, Smokey doesn't automatically kill whoever he comes in to contact with...just most of them. LOL