Golding's novel seems to suggest that moral behavior is often conditioned by society (and therefore becomes widespread through conformity). When the constraints of society are taken away, the impetus toward conformity is removed as well. Moral behavior and morality itself is then in danger of collapsing under the weight of "human nature":
Golding himself has said that the writing of Lord of the Files was "an attempt to trace the defects of society back to the defects of human nature."
Ralph and Piggy are examples of people with an innate sense of civilization and/or a compassionate sense of fairness. Jack and many of the other boys do not share this trait, as evidenced by their eventual decline into savage territorialism and violence.
Given these examples, Golding's novel may be seen to be implying that evil is an inherent aspect of human nature, one of its "defects" that society often masks. Evil is not a result of the boys' hard circumstances, but rather is the default. When the conditions that instill and enforce a moral sensibility in the boys is removed, they resort to "natural" evil and immorality.
As the author once commented, "the moral is that the shape of a society must depend on the ethical nature of the individual and not on any political system."
The social system that trained them has not deeply changed the boys, but acted only as a temporary and superficial curb on their behavior, or so it would seem.
There are, of course, other arguments that may be made on this point. Golding's own words do point to such a conclusion, however.