Recently, I was with someone who was going through a tough time. I no longer believe in the church and am unsure of my feelings about Jesus, but I understand the doctrine. Your son sounds like he may have feelings similar to this person. My active, believing husband was in the room.
I feel very stongly that God loves each of us. I asked this person if they would like a blessing because it might bring them comfort. I expected they would say no and they did, but I can't imagine Heavenly Father saying no to a blessing like that when it might bring them comfort or understanding.
Sometimes I think people are too worried about the correct thing instead of the right thing.
More important than asking if it is appropriate though I think that it is more important to ask if you are offering out of love or out of changing him. They are not the same thing. You can want to change him because you love him, but change has to be his choice and if he feels your desire for change rather than your desire for love it will put a wedge between you.