Father James lets Lincoln know he got Alvarez out of the city and asks him if he's ever heard how Sal Marcano wound up running the city. He goes on to explain that he sold out his own father, watched him die. Then he killed every man standing in his way, butchered them, and everyone else who thought was a risk, warranted or not.
When asked how he knows this, Father James admits that the sanctity of the confessional isn't always so absolute. He explains that he accepted that Sammy and him are criminals, but there's a difference between being a criminal and being a Sal Marcano. He's worried what Lincoln will do once Sal is gone and no one is standing in his way. He advises him to not let this change the good man he knows he is.