The boy with the mulberry birthmark's disappearance has very little impact to the general plot. His disappearance during the fire does, however, serve as a fierce and ugly wake up call for Ralph, who realizes the severity of their circumstances--the whole island experience became a lot less like the fun adventure he had imagined only hours earlier. In the next scene, Golding shows Ralph working exhaustively to build shelters for the boys, even though no one else but Simon has helped him. The loss of the young child in the fire has made Ralph feel more responsible for the littluns in his role as chief, and the shelter building scene in chapter three reveals Ralph's concern for their well-being.
The little boy's death may not have had a huge impact in the overall plot, but it did affect Ralph's take on leadership and responsibility on the island, which does ultimately lead him to clash with Jack over the need to maintain the signal fire.