Desmond has vision of "Not Penny's Boat" after Charlie crashes car into marina

In the car, Desmond and Charlie hear Drive Shaft's hit song "You All Everybody" on the radio. Desmond is not impressed by the song. Charlie then gives Desmond the choice of either getting out of the car or to let Charlie show him what he's been talking out. Charlie then grabs the steering wheel forcing the car into the marina, the same one where Desmond and Penny docked their boat and where he was shot by Ben.

After the car is submerged in the water, Desmond frees himself but Charlie just sits in the passenger seat with his eyes closed. Desmond makes his way through the open window and surfaces, but only takes a few deep breaths before going back for Charlie.

Underwater, Desmond tries to open Charlie's door, but can't get it open. Charlie opens his eyes slowly, turns toward Desmond and places his palm on the glass. Suddenly, in flashes, Desmond sees Charlie from the season three finale "Through the Looking Glass," pressing his hand against the flooding com room of the Looking Glass Station that says "Not Penny's Boat."

After a moment, Desmond snaps to, opens the door and brings Charlie to the surface.

So it seems to have taken a life-altering experience in order to cause Desmond to have a clear vision of the original timeline, much like Charlie's almost dying on the plane which was similar to him being on the brink of death after Ethan hung him from a tree in season one. What does it all mean though?

Ben shoots Desmond, doesn't shoot Penny, gets beaten up by Desmond

Back at the marina, Ben stops to look at Penny on Desmond and her boat named Our Mutual Friend. Ben starts to pull his gun as he passes Desmond getting groceries from the trunk of a car. Desmond yells at Ben "Hey, what are you doing here!." Ben turns around, pulls the gun and shoots Desmond. The bullet hits the groceries and a carton of milk but as Desmond is falling to the ground, no wound can been seen on his body. Penny starts calling Desmond's name as Ben approaches and tells her not to move and "not another word."

Ben says "Hello, Penelope. My name is Benjamin Linus. I'm sorry that you're caught up in the middle of this thing, but your father" and that Penny cuts him off. She tries to explain that she and her father have relationship. Ben tells her "Your father is a really terrible human being. He's responsible for the killing of my daughter. That's why I'm here." At that moment, young Charlie Hume emerges from the boat calling for his mother. Penny tells him to go back inside and then pleads with Ben to not hurt her son. Charlie calls for his mom again and Penny yells at him to go back inside. Ben lowers his gun looking saddened by the sight of young Charlie.

At that moment, Desmond tackles Ben (though it's clearly a stunt double for Michael Emerson). Desmond beats the crap out of Ben and then pushes his body into the water. Ben is bleeding profusely and a trail of blood is left in the water.

So in this scene, we see a continuation of the humanity of Benjamin Linus. He has an attachment to children and abandons his plan to kill Penny when he sees young Charlie. Maybe because he grew-up without a mother, he didn't want Charlie have to grow-up without his mom. Could Ben's care for young kids tie into why the others took the children on the island?