That is quite a conflict. AND you have been given a lot of good advice. I will add my two cents, and you can take it for what it's worth.
You know the father who REALLY wants his son to pick up the football and play sports but unfortunately the son would rather be in show chior? That's a bit what this seems like LOL. Children grow up to make their own decisions, right or wrong. Your choice as a parent is to take a stand and say "this religion is so messed up I cannot support this" OR you can go and say "I will stand beside my son no matter what decision he makes."
Please understand that either one is a decent and good decision and each will yeild it's own outcome. It totally depends on what kind of father you want to present. The religion... is evil. I know this, you know this. Your son... will eventually figure it out on his own, but as of now he's putting forth an effort to something that is important TO HIM.
in my OPINION The greater truth of the matter... the larger picture of the religion does not trump the support a son feels seeing his father in the audience. Because the "truth" is anything but truth, it doesn't actually matter as much as the relationship between you and your son. He knows you're effort in going, he knows what that means. I personally, would go as late as I could and leave as soon as I could and leave the congrats and how well he did back at home, but that's just me.
Either choice you make will send a strong and good message. But yes... this is a tough one.