Your w will need to end things completely w/the OM and I am not just talking about an affair, but the emotional one as well. That means no contact w/him and the saying "we are just friends"...don't buy into it. That statement is used quite often by the wayward spouses. She has a lot of work ahead of her to regain your trust. She will need to be transparent in all of her texting, emails, etc. If she can't agree to that at some point, then she's still got issues w/the OM.
It's going to take a while to get your relationship back on track and you cannot do it alone. She has to be willing to go to counseling and like I mentioned above, be transparent w/you as well. If you haven't done so, I would set up some IC for yourself and if, and when she's on board, she seek out IC and later move on to MC. However, as long as he is still in the picture...she won't be working on the relationship w/you.
I wouldn't attempt to have another relationship discussion. If you continue to bring up the OM, sure she may tell you she'll end it and then sneak around behind your back. It's a thrill and a challenge to keep secrets like this from the spouse. The less you say for now, the better. Step back, give her space and time and allow her to come to you. Try to keep the focus on you and your life.
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.