I've been rewatching everything with my girlfriend (she's a newbie) and we just got to the first three episodes of season 5 last night.
I saw something VERY interesting.
This is not verbatim but not far off...
Richard said to Faraday in 1954 that "18 soldiers from the American Military came to the island, I asked them to leave and they refused, so I was forced to kill them all."
Daniel then questions Richard, "Forced? Who forced you?"
Richard hesitates then says, "Look you answer to someone, we all have to answer to someone, I do too."
This would suggest that Richard has been taking orders from Jacob. As he has been forever linked to speaking with Jacob, advising the leader on orders from Jacob, etc etc.
But these orders sound far more likely to come from MIB given his speech on how much he dislikes visitors to the island, they come, they fight, they destroy, it always ends the same etc etc.
So I think that with this clear similarity in attitude, Richard is actually working for MIB...whether he knows it or not though is another matter.
I'd also like to add that I don't see Jacob telling Richard to purge Dharma.
Jacob has only given us the impression that he wants people to come to prove themselves as being good. From his conversation with MIB you would assume that:
Jacob wants people to come: The Black Rock, American Military, Dharma, Danielle and her crew, Desmond, Drug Plane, 815, Freighter, 316 etc. He brings people, asks people to come.
MIB doesn't want people to come, he wants them off the island: he'd rather see them dead, he has disdain for the intruders. The Black Smoke protects the island from outsiders, The Black Smoke is tied to MIB in that they don't want intruders on the island. Dharma built a fence to keep The Black Smoke out.
I'm not saying MIB and The Black Smoke are one and the same although its possible! But I am saying they're on the same side.
So from all of this... why would Jacob tell Richard to kill people who have got to the island?
Jacob is good for humanity and bad for the island.
MIB is good for the island and bad for humanity.