My (sort of) adoptive son approached me ually?

I'm 38/m and I have a son who is 16 and his best friend is 16. We've known his best friend for a while and we know he doesn't have a very good home life (his parents are devout Christians and he is gay, which they have a major issue with) so we have tried to take him in as much as possible (sometimes he's stayed as long as two months at our house without his parents so much as calling to see where he was). So we've come to the point that we consider him family and I see him as my own son. When he called me late at night to come get him, I came and got him because I heard his parents screaming in the background. When I got there, his mother was throwing plates at him out of the door in the yard (not gl plates, thick and heavy ceramic ones that weigh a good bit) and his dad started cursing at us. I exchanged some words back and we drove on. My son wasn't in town (he was with his school's program) so we had the house to ourselves. So I cooked dinner, we ate in the living room and watched some sports. About halfway through the game, he asked if he could sit next to me (I said sure because he was sitting on the other side of the room and I figured it was to see the tv better). He sat rather close and after a few seconds, he put his hand on my thigh (not my knee, my thigh). I looked over at him just as a reaction and he kissed me (nothing with tongue or anything, just lip to lip for maybe half a second). When I responded badly (which I admit I could have handled the situation a lot better than I did but I was extremely shocked), he just look kind of confused and told me that I must have wanted "it" (by "it", I guess he means ) because I wouldn't have been so nice to him for no reason. Immediately, I felt horrible because clearly he has no concept of people just being nice for the sake of being nice. So he went upstairs and I heard him crying in the bathroom for a while (and then I guess he went to sleep). I didn't go speak to him because I just really have no idea what to say to him to resolve this issue. I don't want to hurt him but for obvious reasons, I would never consider such a relationship. Please help. Thank you.