Your feelings are always justified. It’s fine to feel uncomfortable and a little threatened. And it’s fine for you to tell her. It’s also fine for her to want to see an old boyfriend, and for her not see him because she doesn’t want to upset you.
I think what’s confusing you here is that you want everyone to be happy, and in relationships, compromises and deals struck are often what makes them work in the long run. One way or another, one or both of you are going to feel uncomfortable and possibly anxious. But feelings are just that — feelings. You can’t live your life by them. You can acknowledge them, but your behavior is more important than your feelings.
So, given what you feel, you can tell her you’d rather she not see him, or you can tell her you’re not comfortable with it, but if it’s just this once, you’ll deal with it. You can also ask her if she thinks this is going to be a long term thing, and if this boyfriend is going to become part of her/your social circle or if it’s just this once. Or, you can tell her that you’d like to go with her to have dinner with him. Then again, she may hear your concern and decide it’s not worth upsetting you to get together with him.