FINAL SCENE - SPOILERS - Do you really think he would . . .
. . . just kinda give up like that? I don't think they established enough about the Chief's character to explain why listening to Book's speech about "Are you gonna kill him? Are you gonna kill her?" would cause him to react the way he did, and stop and hand over the gun. Here's a guy who is taking $22 million worth of drugs, 550 gallons worth, and spreading it all over the lovely city of Philadelphia, without consideration for the destruction and ruined lives all these drugs will cause. He first has a fellow police officer killed because of it, and then orders McFee to do the same thing to Book because of it. Then he orders another police officer - McFee's partner - to be killed as well.
Why would he all of a sudden get religion, so to speak, stop and be overwhelmed by the enormity of his actions thus far and let Book go? I mean, if it were me, yeah, I have a sense of justice and fairness, right and wrong, so when Book says, "Enough!", it would sure as hell work on me. But this guy's a stone-cold blooded killer. Why should it work on him?
And if he's willing to kill three police officers (two of whom are already dead), don't you think he would have at least threatened to kill Book's sister and kids to get Book to come out? That would have gotten Book to stop, and pronto, even if he wasn't willing to really go through with it. Just imagine - he arrives at the Lapp place, and calls out, on a bullhorn, "Book, we've got your sister and your nephews. They're all perfectly safe, for now. But if we don't check in within the hour, I have people who will change that situation for the worse. Come on out, let's talk. It's over." That would get Book out of that farmhouse in a hurry.
I asked the doctor to take your picture so I can look at you from inside as well.