Damn Doubting Thomas, that seems like a real difficult situation.
If I was in your position, preventing my kids from getting religious indoctrination would be my top priority and anything else, including reconciliation with a religious wife, would be a secondary priority.
But of course it is a delicate situation, a happy family is obviously important for the kid, and with the added threat that your wife might attempt to flee the country and take the child with her, means you need to tread very carefully.
The "some people believe" line is a good one, you can also try to bring in some of the more absurd religious claims in Islam like Muhammad riding on a flying donkey to heaven and say "some people believe this...", and then follow it up with "what do you think?" or "does that sound believable to you?" Try to get him to think for himself about this stuff from an early age.
In terms of your wife trying to kidnap the child and flee to another country, she can only do that if your child already has a passport, she can only get a passport for him with both parent's consent. If he already has a passport then make sure you get hold of it and keep it somewhere she does not have access to.
Maybe a book like this would be good for your son: In the Beginning: Creation Stories from Around the World