If I were counseling this little boy, I would tell him that God loves us. He knows each one of us. His Son, Jesus died for us to remove the guilt of our sin.
None of us knows the full heart or intentions of anyone - only God knows that. If this boy’s father ever reached out to God for forgiveness through Jesus, then that father may well be in heaven. But, only God knows and only God can judge. He is a perfectly fair and righteous judge. This is our hope.
Only Jesus can remove the guilt of our sin. I would talk to this child about his relationship with Jesus - and, that as believers, we need to share as best we can the good news of the Gospel with family and friends because none of knows when our time to leave this life will come.
I realize the pope did not have the time to go through all of this with this child. But, he could have arranged a time to meet with this boy and his family for comforting them and counseling them - if he could not personally do this, he could have arranged for a minister to call on them.
He could have hugged this child and told him that his question was a very important one and that he would like to talk to he and his family about it, but in a more private setting. I’m sure the boy’s family would have been glad to meet with the pope at any time he said.
Then, he could recite some of the Beatitudes, which outline who is "Blessed".
"Blessed are the merciful, for they shall obtain mercy."
What a beautiful promise. It could comfort the boy's heart.