You have a dilemma, that's for sure. I hope you are involving your son in the discussion of obligations, friends, feelings, commitments, etc.
That said, I have to say that the most important part of the bar mitzvah ceremony is the SERVICE at which the young person becomes an adult in the eyes of the Jewish community, taking on the responsibilities and obligations in the synagogue and in the Jewish community. I hope that you and your son will attend this to support the friend. Every service is open to the public - synagogue members and everyone else.
The party is a celebration but is almost entirely secular. Sometimes there is a blessing, and a candle-lighting ceremony that honors family & close friends and makes references to the study & preparation, but that's it. I think you need to be sensitive to the mother giving numbers to the caterer, and you should consider arriving late but making it clear that your son will not eat the dinner (which will be over) but will just come late to help celebrate IF THAT'S OKAY WITH HER. Your son should participate in selecting an appropriate gift as well, in honor of the friend's significant milestone.
I think it is GREAT that the family is not going overboard with the celebration - it sounds like they have their priorities in the right order, and that their emphasis is on the religious aspect and the Shabbat service. I sincerely hope that both boys on the team and their parents will attend the service to witness the achievement and honor, and show that they are not just in it for the party.