This is a good question. If you want to argue that Boo Radley lost his innocence by killing Bob Ewell, you can make two points.
First, you might want to look at the development of Boo from the beginning of the book to the end. In the beginning of the book, he is a complete recluse. He does not come out of his house and he is presumably filled with fear. The best he can do is sneak around and put in gifts in a knot-hole. At the end of the book, he comes out into the public by protecting Scout and Jem from Bob Ewell. There is a step of maturity, which is a step towards losing "innocence," especially as he saw how evil a person can be by attacking even children.
Second, you can look at the sheer dynamics of killing a person, no matter how warranted it is. Boo will have to live with the fact that he killed someone. Also when he considers why he had to do this, he will remember that the world is not all well.