Theory:
The think that after the war is over, Whitebeard will have died. I believe this for a few reasons:
1. During the story, no one dies (well, people have died like Roger and Tiger Fisher have but they were only mentioned and the deathes were not seen directly). Whether this be Oda's perference or the fact the Luffy's justice is ruining his enemies dream rather than ending their life or something else entirely, I don't know. However, having the story go by without one death is unlikely. Eventually someone has to die and since it will be the first in the manga, it will most likely carry a great level of importance. Some say Ace or Jinbei but having Whitebeard, the strongest man in the world and a yonkou, die would be huge. This leads me to my next point…
2. This is from chapter 529:
[hide]Jimbei: I'll never forget that day… as long as I live......!!! // ......With that one declaration of his, suddenly there wasn't a soul as could lay a finger on Fishman Island...!!! // .........The sheer power of it…!!! .........!! // That man's protecting any number of islands with the power of his name...... / He ain't the kind of man you can just take down 'cause he's a pirate boss.........!!!
Jinbei (referring to Whitebeard): If by some horrible chance...... that man actually... died... what would become of the sea...?!! The Government should damn well be able to imagine that much!!![/hide]
What would become of the sea? Foreshadowing much. Whitebeard's death would send the New World into a frenzy. The balance of power would be thown out of order. This seems like a very ominous statement that wouldn't be said without a reason. Why would Oda have Jinbei say this? Just to have him speculate? No. The whole Fishmen Island conversion had me thinking: The Fishmen Island arc will likely be long and well-planned (perhaps not central to the overall story, maybe similar to Sky Island). It has been hyped up since Arlong so I think their will be a major conflict and battle waged (I believe the same in true with Elbaf). Jinbei mentions that thanks to Whitebeard, the island is in peace and not a chaoic place compared to previously. However, with Whitebeard gone, what will happen? A conflict between humans (pirates) and fishmen is sure to erupt with the Strawhats in the middle.
3. The marines are prepared to risk everything in their effort to take out Whitebeard. Having the marines be destroyed now when they have been the central figure of power in the story would be an odd move and would leave many storylines either unfinished or somewhat meaningless. So many storylines tie into the World government (the void century, Dragon's revolution, Pirates vs. Marines in general). So many ascepts of the One Piece World would be altered and it leaves for a very messy situation. Some believe that with Enis Lobby destroyed and Impel Down under attack, the Government will fall at Mariejois (with two of the three bases gone and a battle taken place at Mariejois, it is understandable that they could lose). But for the reasons I just stated, I think they will win. Therefore, since they won, Whitebeard will have lost and will die.
4. The one to kill Whitebeard will be Blackbeard. Whitebeard must hold a grudge against him because a. He killed one of his crew, his son (figuratively), b. He left Whitebeard's crew to become the pirate king which would mean surpassing Whitebeard himself, and c. He defeated Ace and turned him over to the World government. Having Ace be defeated after being warned by Shanks will enrage Whitebeard because he has only himself to blame for underestimating Blackbeard and he will seek revenge against Blackbeard. Blackbeard on the otherhand has been setup as Luffy's final enemy in the story and having Whitebeard take him out after Luffy's staredown with him in Jaya would be foolish. Blackbeard is the most likely person to kill Whitebeard.