Very interesting question. We obviously don't know very much about what will happen to them. We do know that the novel is set during war time, that there has been an atom bomb that in the first chapter Piggy says has killed a lot of people and destroyed large parts of their country. We also can see at the end of the novel that Ralph does not hide what they have done - he confesses to the officer that two of the boys have been killed openly. However, the officers response in saying that this was "not a very good show" and confirming that they are all from Britain immediately reveals his complete inability to comprehend the "end of innocence" that the boys have had revealed to them by their experiences on the island. He stands in sharp contrast to what the boys have been through: he is civilised, comes from a civilised nation where the pull and power of civilisation over his life is still strong. The boys, on the other hand, as we have had abundant evidence to show, have been reduced to blood-lusting savages, able to perpertrate even the most terrible crimes on each other.
I think, given this, the most likely outcome is that the naval officer will completely blank or ignore the deaths - he is evidently unable to understand them and it would be very difficult to identify any one or two individuals who were guilty alone of the murders. The likelihood is that the boys would re-enter their old lives and civilised ways, sadder at the deeper knowledge they possess about how inherently fragile civilisation is when compared to the deep evil and savagery that they have discovered first hand lies at their core.