Ben isn't the real father, the others kidnapped Alex when she was a baby.

As for Charlie, it was his destiny to die. Remember what Desmond said? "THe universe has a way of correcting itself" and that one lady said about the guy who died "If I told him it was gonna collapse, tomorrow he would've been hit by a taxi. If I told him about the taxi, he would slip in the shower and break his neck."

If CHarlie survived the water sation, he was gonna die by something else. He almost died like 3 times..I think it would get kinda old if every other episode Charlie has to find a way not to die like he's supposed it. He had to die =/