Do what’s best for your son. There’s nothing that will overcome that guilt. Not saying what’s best for your son is for you to reveal the truth now or later. That’s entirely situational and only you know.
I don't think it's fair to consider only the son in this. I'd say do what's best for both your son and your wife. And to me that's pretty clearly telling his wife the truth here.
I think this is right. Many parents could think of choosing to opt out because raising a family can be difficult sometimes, but it’s a responsibility people have taken. Take it seriously. It’s a bit chicken to say “I’m out” whatever the reason. See them through their formative years then do your thing.
The kid will be fine. Couples separate or get divorced all the time for all kinds of reasons. “I have two loving parents who are now separated” doesn’t appear on the shortlist of bad things that can happen to kids.