As you discuss Lord of the Flies by William Golding, you can definitely use loss of innocence as a theme, especially with regards to the character of Ralph. One thing you want to think about, though, is that Golding has a somewhat ambivalent view of innocence.
Although Golding was ambivalent about the Church of England and did not believe literally in the Bible, he still considered himself a Christian of some sort. This religious background is evident in his conception of human nature. He did not consider children purely innocent; instead, his portrait of them shows an almost Hobbesian sense of Original Sin. The instant the children are free of the social rules and conventions of the adult world, many of them revert to savagery, committing horrible deeds including murder.
Thus as you create a thesis about loss of innocence, you might want to discuss how Golding's novel challenges our ideas about the innocence of young children. To what degree did they have innocence to lose and to what degree did they bring evil with them?