I don't think it was the smoke monster impersonating them. I also don't think they were brainwashed or became evil. There has been ongoing issues with babies and births on the island, Aaron's was meaningful as somewhere along the way, according to Ben and the Others, a healthy birth became impossible. Perhaps the ship's crew learned something in the temple about Danielle's pregnancy, that she should not be allowed to give birth the Alex, for whatever reasons, and they were trying to kill her not because they were evil, crazy or doppelgangers, but because they were doing what they thought was right and attempting to prevent an even greater catastrophe.
Is he really trying to change the future or simply saying the things he now knows he must say?
I loved Charlotte's warning to Jim that the island is death, implying that it is diseased or dying, a corrupting influence that will take you with it.