To me, the main moral of the story is that people must not just accept injustice.  Instead, they must fight against things in the world that are evil.

In the book, Luke is a third child in a world where third children are illegal.  He has disagreements with Jen (also a third child) over whether they should try to fight back.  Jen eventually is killed at a protest against the way that the government treats third children. Luke then comes to realize that he really needs to try to do something to fight back.

That is why I think that is the main moral of the book.