Piggy's death is different from the others because it is the first one that is the result of a completely intentional act. The other two deaths did not involve the same clear evidence of "malice aforethought".
The little 'un with the mark on his face was the first to die. His death was completely accidental; he was the victim of the fire that went out of control, and his demise was actually only assumed by the fact that the boys later could not find him. The little 'un's death occurred soon after the boys arrived on the island, before they had had a chance to take count of how many of them had actually survived the plane crash. No one had even known his name, and he was remembered by Piggy only because of the disfigurement on his face.
Simon, the second boy to die, was killed by mistake. Caught up in acting out a ritualistic reenactment of killing a pig, the boys, in their frenzy, killed Simon without realizing it was him. Although Simon's murder was more sinister than the little 'un's in that it was the direct result of the growing savagery of the boys, it was still unintentional.
Piggy was killed on purpose. Standing on a ledge above him while Piggy was trying to reason with the tribe, Roger, scornful of his words, dropped a huge boulder "with a sense of delirious abandonment" on Piggy, killing him (Chapter 11).
First, the littlun with the mulberry birthmark disappears after the first signal fire gets out of hand and destroys a portion of the island. Using technology to plan a signal fire is civilized; allowing the fire to lose control represents destruction, and savagery.
Second, there is Simon. Golding makes it clear that Simon's death is also intentional, but that it is a mob that shares the responsibility of killing Simon. Everyone - even Piggy and Ralph - were dancing in the rain on the beach when Simon comes down from the mountain.
In that particular scene, Golding switches from describing "it" and "the beast" to "Simon was crying out something about a dead man on a hill" - in the very same paragraph. Why else would the author choose to drop Simon's name alongside the vague pronouns and beast references unless that is a clear clue that the boys knew exactly what they were doing but were simply caught up in the savagery of the moment?
Lastly, Piggy's death is the symbol of a complete destruction of the vestiges of civilization. The bigun who pulls the level, Roger, is the first character to test the boundaries of this new civilization by tossing rocks at the littuns at the start of the novel. Therefore it is no surprise to us when it is Roger who pulls the level that releases the rock that kills Piggy; we've watched Roger's utter savagery in torturing the pigs - why shouldn't he be the one who kills the good, brave young man nicknamed Piggy?