Hope you like them...
When Abaddon first approached Hurley asking him, "Are they still alive!?" I took that to mean he somehow had a vested interest in the rest of the Oceanic 815 survivors. Obviously that isn't the case. I feel since he was the one who atleast "organized" the search for BENJAMIN LINUS he represents the Hanso Corp.
They are probably pretty ***MOD EDIT *** that Ben killed off the entire community. So they are going after him.
BUT since communication and arriving to/leaving the Island are odd things they may not be sure Ben killed them all off. They may just know something's up and he's behind it.
Therefore his "Are they still alive?" question to Hurley could mean the Search Party he sent, Ben and the Others, or maybe even the original Dharma Initiative.
Now for Ben's "Man on the Boat", the mole if you will.
I feel this has got to be
Because as even Jack says himself they don't seem to be very surprised to find out people survived Oceanic 815 crash. If they already had a survivor with them this would make sense. Also since he's gotten on and off the island he'd be their expert in the most important of tasks...finding the damn place...
And finally a theory I just came up with as I typed these ramblings...why were the people on the freighter chosen? What if it is because they were all SUPPOSED to be on the flight and thus can survive.
We know the pilot was SUPPOSED to be on the flight. At the beginning the bearded guy was crying when he saw the news of the wreckage being found. That would be a natural reaction if you were supposed to be on such a flight.
What if NAOMI is the only one who had nothing to do with the flight. And that is how she ended up dead?
She didn't belong on the timeline of the Island like the others...