I would argue that Jack's group kills Piggy because he is ideologically opposed to their thuggery and lack of civilization. Right to the end, Piggy adheres to the tenets of civilization, holding onto the conch and fully believing in his right to speak while holding it. This is totally opposed to Jack's philosophy that hunting, not civilization or rescue, is the top priority.
Roger's decision to roll a boulder down the hill towards Piggy, who is close to blind in the aftermath of his glasses being stolen by Jack and his crew, is a malevolent (and successful) attempt to silence Piggy. Throughout the story, Piggy has been a paragon of logic and rationality, and by squashing Piggy, Roger, who is well-known by this point for his evil nature, attempts to squash these ideals.
The violent nature of Piggy's death, and the detail in which Golding describes it, speaks of the levels of malevolence that Roger and Jack had for Piggy.
Piggy fell forty feet and landed on his back across the square red rock in the sea. His head opened and stuff came out and turned red. Piggy's arms and legs twitched a bit, like a pig's after it has been killed.
Piggy, for all his lofty ideals about logic and civilization, is treated with the same respect as the pig that Jack has killed just prior to this conflict. Jack's group kills Piggy because his voice of reason is an irritation to them and simply because they have the power and the wherewithal to do so.