After Roger destroys the sand castles of the Littluns, it is Maurice that feels something about the "unease of wrongdoing" and runs off into the woods, feeling uncomfortable about what they've done. He doesn't like what they've done and his guilt makes him ashamed.
But Roger sticks around, not really feeling too bad about what he's done. He is the one that begins to feel some pleasure about doing things the young kids don't like or hurting them, but he feels some "taboo of the old life" and it prevents him from actually hitting the boys with the rocks he is throwing.
It is Maurice who "still felt the unease of wrongdoing" after Roger kicks over the town of sandcastles, buries the flowers, and scatters the chosen stones in the sand village that has been constructed by the littluns as part of their game. Maurice's guilt over this situation is evidence that he still retains components of his humanity on the island, even without the presence of an adult figure who might punish him. He has a sense of what is right and wrong and is afflicted by the unkindness of Roger's actions. Consequently, he leaves the scene almost immediately.
Roger himself experiences a similar feeling later on in the chapter when he begins to throw stones at Henry. It is only "the taboo of the old life" which ensures that Roger leaves adequate space ("perhaps six yards in diameter") so that he will intentionally not hit the boy. This is a result of heavy social conditioning by a "civilization that knew nothing of him and was in ruins."