FWIW (I don’t presume to be giving useful advice, it is a very delicate matter) if it were me, I would not go out of my way to seek this person. But should it happen that I speak to him, I would ask how he deduces, say, from the assumption that God does not exist, which is an abstract idea, statements such as “eating shrimp is fine” or “stealing is fine”. He is likely to reply that he does not think at all that stealing is fine – because it hurts another human being, or something like that – OK awesome you’ve found many points of agreement, same applies in regard to not hurt another human being etc. As for seafood and sausages, he may say that he likes that food (stay silent, let him draw his conclusions, that he is seeking to justify something he had already decided to do) or maybe he says that he tasted them and they are awful and will never eat again (that’s not the best, but better than some), or maybe he will say why should I refrain? It’s told to us in the Torah, but the Torah was not written by God…. oh wait, which God? let him get into confusion. To such remarks, just reply the discussion should not involve God which we can not prove or disprove, that whoever wrote the Torah appear to you pretty bright and smart and he is free to disagree but has to support his point. Always bring back the discussion to concrete situations and keep asking whether he can prove that a life with the “pleasant” aveirot he lists (tell him to list them) is more fulfilling than one without. From time to time also keep telling him that you greatly respect decent atheists and that the same respect is taken for granted in return.
I don’t think it will change his outlook but I do think it will help him feel he is being taken seriously, it may make him think (and possibly change his mind about some very minor details, but who can weigh a seemingly small mitzva) and given the situation with his son, it is very important that he does not go “out to battle” against the observant people, if you can convince him the world is wide enough for all sort of people, life for his son will be much easier. Be Hatzlacha.