I'm kind of baffled by your question. I guess I don't understand why you WOULDN'T let her know that you are aware of her affair. Did you read your wife's note to the OM carefully? She even tells him to "be a man" at one point. Do you think she'd say that a "man" would sit back and say nothing if he knew of his wife's affair?
You seem to think that "confrontation" means something more than being direct and honest. I believe in honesty. She should know that you know of the A, and that you won't tolerate it. Period. There is no "confrontation". It's just two people having a frank discussion about their relationship and their personal boundaries.
If your wife's affair has fizzled out, and she drags herself back to your home, reluctantly, what would you then discuss with her about her affair? How do you think she will react if you casually mention that you knew about it and sat back, passionlessly, and said nothing? My wife thanked me for fighting for her. Would yours?
It sounds to me like your wife is getting the brush off from the OM. Perfect time for you to let her know you won't tolerate an open marriage. She's running out of options. Be that strong "man" that she needs.