If you two never actually agreed on anything vis-a-vis dating while you were separated, I would merely wait until the next time she brings up in conversation something about "I wouldn't want to be with anyone else right now," or "I'm not seeing anyone else right now." Then I would put my hand up and say "PLEASE STOP IT. We both know you're lying to me right now, and it's incredibly disrespectful to me, to our marriage and to our family. I know all about you and ________ , and I'm no longer going to stand here and listen to you lie straight to my face. When you're ready to deal with our issues truthfully -- and I would hope that even if we divorce, we would continue to teach our kids the importance of families telling the truth at all times -- then we can have a conversation."
Until she actually ASKS BACK INTO THE MARRIAGE, there's not really much more you can do other than not allow her to lie to your face anymore.
It would also be perfectly reasonable to let her know "I have decided that I'm no longer willing to lie to cover up your affair."
