I think confrontation is what you need SL. You wife says she had no respect for you. Do you think silently tolerating the OM in your W's life, is going to make her magically respect you?
The question is what kind of confrontation - clearly you can't have an angry discussion. I believe there are ways of handling this. I think you have gently, but firm bring up your concerns about the emails, text and flirting with OM. Because he is her Boss, you will have to decide what you can live with before the discussion starts. I think you have to be clear in how this makes YOU feel. She has all the facts, so it's easy for her to dismiss it if nothing is going on.
Honestly, I think it's your wife's best professional interest to stop thing with her boss. Even if it totally harmless, it's playing with fire. I don't care if he was an HR lawyer (they can do stupid things too) Ask if her this, if there was a problem and all these texts and emails went before a jury(and they would), how would they look? Still harmless? I've read enough cases where what some people considered harmless got a lot of people in hot water.
First any discussion is going to automatically put her on the defensive. Know that going in. If she is truly doing nothing then she will feel like you don't trust her, etc. If she is doing something they she may try to downplay it or dismiss your concerns. But you have to get through that initial response and keep your cool. Keep hammering home your point. If you have to make a central theme in your mind and stick to it.
Lastly, if you are worried about not thinking clearly or reacting in front of your W. Practice what you are going to say OUTLOUD. In the mirror, in the car, in the shower. Start by writing it down if you have to. Try to imagine her responses and address them If you have practice it enough times, when you really have the talk you can be clear and focuses. I do this all the time.
Remember, this is my view there are lot of differing views. Some go further than I would by exposing the EA to the OM's W. some say do nothing and let it fizzle out on its won
Patience is bitter, but its fruit is sweet. --Jean Jacques Rousseau.