As others have suggested, it is a good idea to be compassionate toware your W, but you also have to treat yourself well...
"Sweetheart, I'm very worried about you. I found this pregnancy test, and whether you are pregnant or not, it must be an incredibly hard and stressful time for you. I'm also worried about me. This is quite a shock and it is unhealthy for me to keep it bottled up. I feel sick finding something that confirms a PA when you denied that there was one. I am scared for our son and his mother. I am scared for myself, I'm not sure how I can continue to live like this. Whatever happens, I really want to be able to be open and talk about this so that we have a chance to have a healthy R, whatever kind of R it turns out to be. We both deserve truth and compassion here."
At the same time, this is HER problem, a result of HER choices, and you need to not fix it for her. There is nothing wrong with letting her see your anger and pain. And, if you are starting to see just how serious a problem her continued contact with OM is, perhaps you will reconsider putting a boundary in place there with which you treat yourself decently.
As long as you tolerate it, she will keep trying to manage her feelings and OMs feelings so that she doesn't have to confront the fact that "her true love and destiny" has turned out to be a momentary panacea with nothing really left over at the end, not even friendship, not even someone she really likes. This isn't to say that she wasn't getting something she needed and wanted from the A, BTW, only that it wasn't what she thought it was.
Let her see your pain and anger. You are doing no one a service by burying it, you are letting her continue as she is, which she hates. And, beyond all this, I'd be especially pissed off because she is putting so much of the barrier to intimacy on you when, if she could be honest with herself, she'd have to admit that her guilt, fear, and continued lies around her cheating is a huge part of it. If you are unsure you want to continue, she should know that.
Quit coddling her, if nothing else it enables her to coddle OM.
