I agree Keith, you are right. No one spends a lot of time with an ex without there something going on. And you are correct in asking her to stop seeing him.
Your wife is doing a very classic head game with you. She is trying to assuage her guilt by making this about you and your trusting her so she doesn't have to change and face her own faults. She is doing very little to gain your trust and hold on to it. If she is spending time with her ex, then something is going on and you are right to suspect her. But she is trying to say it is about you. It is not. There is no reason for her to be with her ex. If she has indeed "been there done that" then she would not need to be with him, at all. She would leave him in her past. And she would make the choice to be with you.
Your wife is not putting your needs first, as she should be doing. Every marriage needs to have trust and the partners need to put each other first. If they do not, then the marriage breaks apart. Your wife is putting her needs before yours but you are doing as you should and putting her needs before your own. That is why you are suffering and your marriage is focused on her and her alone.
If you are feeling that you are in the way, then that is a sign something is wrong as well. You should not feel that you are in the way in your own marriage.
You can always go back to the therapist with your wife and tell her the truth of what is going on. It would be up to the therapist to sort it out and decide how you should handle it. But if your wife is not willing to change, then it may have no effect. I am sorry, but you may have little choice but to either accept that your wife will not give up her ex, or you may need to try a separation. Sometimes, separating helps the other person finally see the effects of their behavior. You may want to consider it. It may also help you to see a therapist to help you decide if this is a good move for you.