I think she's saying she could really make things ugly if you are jerk about it because she is scared too. She is probably in a state that feels like a holding pattern, she doesn't want to let you go or set YOU free, but she doesn't want to continue down the path of unhappiness that she feels. Furthermore, yes, she doesn't want a repeat of another ugly divorce, and is emboldening herself to not let someone do the underhanded thing the last guy did to her. You get it though. You are a much better person than that, and that's exactly the point...you don't have to be a jerk about it. I received advice from several people, and the consensus was, be a gentleman during this time. Don't be a pushover, but be a gentleman. I think this is much easier to do if you focus on the three major things, the kids, the kids, the kids. It is about the kids first and foremost. You need to have the heart to heart with her like you were talking about, but in the context of, "this isn't working for me, you, us, or the kids any longer." We're all miserable, and we can't keep going down this road. Everyone kept telling me, this kind of situation can be as bad as you want to make it, or as cooperative and cordial as you want to make it, assuming you both are mature enough to conducct yourselves well. I can tell by the way you write and the way you mostly "get it" about setting her free that you are.
I was always upfront with my ex about anytime I was going to meet with a lawyer, and any drafts of our dissolution agreement I always had her examine first. If you maintain setting her free is the way to go, you both have to admit things are not working and that you will both cooperate into seeing a dissolution agreement through. But YOU should do the bulk of the work on it, set up a custody schedule you think is fair, set up what you think is fair for child support relative to the time you spend with your kids, how much you pay for daycare as the primary breadwinner, and so on. Give her an offer that's fair for both of you, make it as much of a win-win situation as you can in a situation which nobody really wins. Just keep the kids in mind first and foremost. Then, with her awareness, take it to your attorney and have him review.
I really do think you have to do this to set her free. She IS telling you she wants out, but she doesn't want to be blindsided by activity she thinks is going on between you and an attorney. I think she wants to be a part of getting out of this uncomfortable situation with you, not without you. I would talk to her and see. If she balks about going through with this, then you reiterate, "look, I'm confused, if you don't want to go through with it, do you really want to keep going on like this? I cannot and will not keep going on like this."
Apparently, all the right answers to these problems are to indeed do the things that are counter-intuitive. Hard to do, but from what I can tell, you two are planets apart, not just miles apart at this time. The intuitive things don't work at a time like this.
As far as being her friend, just think of her like your best male friend at this point. If you don't feel like doing something for her, don't. If you do, then do it. You wouldn't bend over backwards all the time for a buddy of yours, nor would you plead and chase a male friend to come back into your life. You also wouldn't "go dark" on your best male friend either unless he did something just completely unconscienable. Treat her almost the same as you would your BEST male friend.
Yes, you probably should keep the OM issue out of it, but don't think for a minute there isn't one. You're closer to her than anyone and you know when things aren't right. But it's kind of like living in a old house with suspect plumbing, and standing downstairs in a room that is directly below an upstairs bathroom. By the time that something "bad" is leaking through the roof and makes its way to your attention, you can be darn sure that when you go up there to investigate it's going to be much much worse, because you still went ahead and trusted that bathroom plumbing even though you knew it was suspect.
Sorry, all I know how to do is write questionable metaphors.
Point is, this suspicion alone is enough to cause you enough anguish to not tolerate things any longer. What if your son was 12 and saw this going on? How might he look at you? You can't go on like this forever. And you should take the initiative to do something to stop it. That initiative I beleive is the lawyer and setting a dissolution in motion, because it is the only thing to show you are serious enough to demand your dignity back and to allow yourself to be away from someone who has clearly expressed they don't want to be with you.