Appreciate your heart to reach out to your aching atheist friend. The rule of thumb in attempting to minster to people with stories of pain and suffering is to fight the urge to give them quick intellectual responses. Though the question itself might appear like one that demands a good rational response, the questioner behind (as Raviji, taught us) is crying out for emotional comfort, especially if its a personal question and not one posed on behalf of others.
So listening and allowing them to empty their chest goes a long way in helping them to start with. Since this is a childhood friend I’m sure you’d have done that amply. I also like the fact that you started with some ‘secular’ answers and didn’t immediately start supplying Scriptures.
When they know we care enough to listen, they know we care. And such people never care how much we know, but clearly know how much we care. Be compassionate, be consistent, be committed, be patient these things come in multiple layers and are not overnight projects. Never give them the impression that you are doing all this, to convert them to Christ. Be clear that you are with them, regardless,
Now coming to the use of Scriptures. Sensitivity and Sensibility are key words and attitudes here.
Your friend is struggling with issues of injustice, unfairness, rejection, lack of sense of belonging, lack of love, issues with identity - so these are some of the areas that you might want to touch upon and establish gently through the scriptures.
The idea of belonging, to the Father, created with intentionality, care and purpose are very big and comforting ones (Psalm 139). The idea of being made infused with value and worth in the image and likeness of God is another big one. The need for not having to do work or earn or shape identity and the affirmation that come from realizing the, ‘who I am?’ question tied and rooted in the ‘Whose I am?’ are all very powerful and life defining motifs. The idea of Salvation, as son-ship through adoption is very deep too. Also the idea that our parents here, are stewards and God indeed is our Father in the real sense, could be hugely helpful.
Psalm 27:10 - Though my father and mother forsake me, the LORD will receive me.
Isaiah 4:15 - Can a mother forget the baby at her breast and have no compassion on the child she has borne? Though she may forget, I will not forget you.
And your own approach of the Genesis families, is a helpful one too.
I pray that your friend finds meaning and value in what you share about the (his) good, good Father in heaven, who sent his only begotten Son, to redeem him (you friend) back to life and given him fullness, purpose and joy would strike a deep chord, in Jesus’ name! Amen.