Didn't the writers already say that they are not going to take the "alternate reality" route on any of the story lines? I thought that was stated.
I think Jack is just fucked up. He says something like "go upstairs and call my dad" and the doctor gives him a weird look.
That shit with Charlie is shaky. He could have easily ran out of the room and locked the door from the outside, or just ran the fuck out, jumped inside the huge pool, and swam to the boat. That shit was suicide, but Charlie isn't suicidal, he has a family now. I guess his rationale is that if he doesn't follow Desmond's vision, everyone else won't get rescued, so he martyred himself.
The thing with Naomi doesn't make sense to me either. We know she wasn't part of Penny's search team. I'm guessing she's from the Dharma Initiative, and they want the island back. What I don't get is how she had the picture of Desmond and Penny, and why we never saw Desmond question her about it.