I think out of respect for you she might want to consider taking a break from this other man while you work through the trust issues that she has brought up in your relationship. It's not fair to come to someone and tell them that you have been lying to them for however long but that you're unwilling to change anything to help rebuild that lost trust.
What makes you uncomfortable about this other man? Is it just that she has been having an affair with him? Poly requires a lot of communication. You both need to talk about what you need and how you feel. It's not about someone having their cake and eating it too while anyone else involved stays quiet, regardless of how they feel.
Hope that helps a little