I mean--I would never tell my SO that they had to end a relationship with a friend or whatever.
I'd tell her that it bothers me. That she had said it would end and be over with, multiple times and, in the first instance she kept talking with him secretly.
She can say it wasn't a secret and I'd agree that she didn't go out of her way to keep it hidden...but she obviously failed to mention it over the course of months and I find it hard to believe that, in the time you've been dating, it never occurred to her to mention the messaging or anything which comes off to me as a lie of omission because she knows it's dishonest.
So I'd just tell her that she is free to do what she wants but it bothers me and creates a dent in the trust because, IMO, she kept it hidden from me and then didn't end it after, twice, saying she would.
I'd honestly be more curious why this relationship matters so much to her that she's willing to damage our trust and our relationship over it.