Ralph weeps for innocence for several reasons. The first is that Golding uses Ralph's moment to express the pent up emotional release of the novel. Ralph weeps, because in this moment, that particular emotional outlet is all that is available to him. Ralph's crying is all about emotional release, and all of the hardships and terror he has endured suddenly comes rushing to the forefront in the reassuring presence of the naval officer.
He weeps for the loss of innocence, because he realizes the tremendous toll that the island has taken on all of the boys, robbing them of their childhood and leading them to commit heinous acts that normally none of them would have commited in the protective confines of civilization.