Dear Justice One,
A quote: "And as for his reaction... he has known since childhood that his Dad has a sick and twisted sense of humor. Besides, it kinda removes all doubt when he continued and said something to the effect of "just because I'm disfellowshiped, doesn't mean I don't think its not the truth." '
My advice, for what it is worth, is first, sincerely (emphasis on sincerely) apologize to your son. Tell him that you did not MEAN to disrepect his beliefs. I think that anything less than a sincere apology would indicate that you are less than respectful of your son's ability to make choices for himself. This would - naturally - put up his back and make his defense alarms go off big time.
You implied that you have a certain "sense of humor" that your son should now. Maybe he has known, "since childhood" that his dad has a certain type of humor, but he may find it offensive. Have you ever asked??? Out of respect for you, his dad, perhaps he has never dared, and will not, now. But it's something you should consider...
As a dad, perhaps your approach to this son has been not quite on the money. Worth considering. Final words, bitchy as they may be, do you want your son back, or do you want to be "right?"