If it is killing you to fake it then stop faking it. There is zero benefit to you for keeping her secret, even from her! I mean she knows she's having an affair, so why on earth are you trying to hide your knowledge of it from her.
Sure, you can put it in your divorce response but what difference does it make if that is a surprise to her or not. And I doubt there will ever be a divorce response because as you can already see, she is backing away from the brink of filing because her affair is clearly not a viable exit plan.
I think she will never file or voluntarily leave if she doesnt have to because right now she has everything she could possibly want, filing for divorce is hard, it would make her the bad guy, and there is no rich prince charming out there that she is trying to chase down.
I think you either need to file first, with all salvos, or you let her know you know everything about her affair. If she wants to play dirty from that point on, you both know that you have your ammunition to fight back if needed.
If there is only one thing I can just about promise you, its that you, and your kids, will feel immensely better when you are not holding on to any secrets.