I just noticed this in the conversation between Naomi and Abaddon.
Naomi: There is only so much I can do.
Abaddon: Your modesty is positively charming.
Is this a hint that Naomi had some sort of "powers" too?
Yeah, I wondered the same thing. Also, because she apologised with her dying breath. I think she had some kind of Power that was supposed to keep the others safe.
She probably knew she was going to be going up against a lot of people on the Island and felt like trying to protect a bunch of geeks was going to be rather difficult.
The scene between Naomi and Abbadon seemed to indicate she was some kind of mercenary, she was the one with the military training who was supposed to protect the four team members, but Locke killed her and screwed the freighties plans up.