FAQ for
Gone Baby Gone (2007) More at IMDbPro »

The movie is largely the same as the book. The changes made largely consist of condensing scenes for the sake of time. In addition, Helene McReedy is more sympathetic in the film than in the book. The character of Cheese is changed from a white imprisoned drug dealer to a Haitian who is free and a sub plot involving a gang war is eliminated. The most significant change is Angie Genarro who, due to scenes which were truncated from the book, becomes largely a cypher.

...charged with the murder of the pedophile?

While Patrick's actions may have technically been illegal it must be remembered the circumstances in which they occurred. In the middle of a massive shoot out in which the occupants of the house were trying to kill Patrick and the police Patrick kills a man who had taken part in the brutal rape, torture and murder of a young child. The police are not going to investigate the crime too much and likely ruled it self defense.

Even though the pedophile was shot in the back of the head proving that Patrick wasn't being confronted by the pedophile