Defeating Jolly Roger once and for all would destroy the game. If he was destroyed, all the skeletons would be gone, all the quests involving skeletons would be editted (virtually destroying the Black Pearl quest,) all the invasions would stop, and the game would be nothing compared to what it is with Roger. When the quest says "the only way to defeat Jolly Roger," I'm pretty positive that means, as in, winning a fight against him, sending him in to hiding again, and etc.
Besides, we're pirates. If Jack wants a Cursed Blade so bad, he can go plunder it himself!
