Ray,
Whether you realize it or not, you are now FULLY engaged in theocratic warfare.
Your son already goes to meetings, right? Your wife will spend the time you are at work humming him kingdom melodies right along with lullabies and reading him My Book of Bible Stories right along with nursery rhymes and Pokey Little Puppy.
DO NOT JOIN THE BORG. Rather the most important thing you can do is to teach your son how to reason. Talk to your child as you spend great, enormous even, amounts of time with him. Don't let your wife be the only one who speaks to him of spiritual things. Talk to him about what you believe and why. Tell him what morals and values are most important to you and what your hopes are for him. Don't EVER let Jehovah (or worse yet the elders) become the father he never had. You absolutely do NOT want him feeling like he can only talk to Witnesses (Mom, the elders, his JW friends) about spiritual matters.
Meanwhile, I think Path's advice of broaching your earnest questions to your wife. "Honey, I know it would be much better for the family if we were all the same religion, but here's something that really puzzles me...", "I just can't wrap my mind around ...", etc.
And joelbear's advice to keep your family busy doing things together is excellent! PARENT your son. Many fathers do not. Also, use your headship to your advantage. Your son IS allowed to participate in sports (you may want to limit it to TOWN rec leagues rather than those like YMCA with a religious connection, in deference to your wife's feelings, however), your son CAN join the Math Club, Cub Scouts, the school Chorus or Drama Club or Band, etc. Your son WILL take college preparatory classes in high school. Go to Homecoming, the Prom, etc. He will NOT be a freak, and he is under no obligation to buckle under to pressure to NOT celebrate holidays or birthdays at school unless his own conscience requires it of him. You have no idea what a gift you will be giving your child if you merely allow him normalcy.
Best wishes for success,
outnfree