I agree with you about Jacob (or some other major force on the island) using the images of the dead as a tool to influence the living. But I believe that these are only illusory things, not really the souls of the dead. That would explain why Claire was with Christian even though she might not be dead (we don't know).
I just don't think there's any evidence to support the whole inclusion of souls into the LOST storyline. I mean, it's pretty complex already without bringing the afterlife and religion into it. That would be really hard to explain scientifically, which is what the creators have said-"Everything can be explained with current (if theoretical) science." They've said it a few times.