As I read your post, I hear three separate issues to address:
1. Ensuring your DS understands the language and context of the bible, including the historicity of the writing and the subjects/events contained therein.
2. Giving your DS the tools to evaluate the veracity and validity of information/beliefs.
3. Building the social intelligence to respectfully discuss sensitive topics with others.
On the first count, I can offer many good resources on biblical interpretation and theological tradition from a Catholic or a neutral Christian perspective. There is considerable divergence in opinion among the various Protestant denominations and Catholicism, and it pays to find trustworthy resources to inform the learning process. I assume from the tone of your post that your family is not particularly affiliated with one faith. What is your openness to your son exploring and, potentially, choosing a faith that is not your own?
On item two, religion is a unique beast. He might really like Thomas Aquinas' Summa Theologica, which is essentially a series of philosophical arguments and logical refutations made to form the underpinning of essentially all Christian faith. Even if your family isn't Catholic, Aquinas does a masterful job in his treatment of the existence and nature of God. (As my name suggests, I am an ardent fan.
On point three, I think the key is to cultivate an attitude that the vast majority of people are good people seeking the truth, and that different life circumstances, experiences, and abilities create situations where people can reasonably choose different beliefs. The fact that such a large share of the world subscribes to monotheistic faith is, itself, a remarkable confluence of belief! Encourage him to speak politely to others, and actively foster a perspective of being a student. If he sees exchanges with others as opportunities for personal growth, he will be more humble in his approach. Ask questions, find a good spiritual director to field his questions and model theological debate.
I love that your son is finding this interest himself!
