What is Cormac suggesting when the boy begs his father to be merciful to the strangers the meet.

Certainly the boy radiates empathy. The boy seems to hold the last vestiges of humanity left in this fallen world; the boy is hope. Indeed the father says in his narrative that, "All I know is the child is my warrant, and if he is not the word of God, then God never spoke." I wouldn't go as far as to say the boy is God but he seems to be a Christ figure of sorts. In a world that has become Hell, the boy reaches out to strings that might harm him. He truly personifies hope on a damned planet.