RC, please take some time to breathe deeply and sit with your feelings. What I have found is usually the case in man-woman relationships is this: although women are always considered to be very emotional and all about their feelings, we tend to think a lot. A lot, a lot. And what happens is we often verbalize what we're thinking as a way to work it all out. We're very mentally involved and speaking about what's in our heads is a way for us to look at it, wrestle with it, feel like we're not alone, and come to terms with whatever we're dealing with. Now, as someone mentioned earlier, men have a tendency to see themselves as rescuers or "Mr. Fixits" and they often assume that when women start talking about what's going on with them, that some remedy must immediately be found.
I am writing this to tell you: NO-O-O-O-O!!! Nothing could be further from the truth. Oh, how many times I had to tell my ex to stop giving me feedback and just listen. I think, probably because men are usually such do-ers, women just want them to stop and hear them. Just hear them, know what they are struggling with, and find some empathy. And eventually discuss. But jumping to conclusions and thinking some rash action needs to mitigate disaster from the ramblings going on in a woman's head isn't exactly practical. It's reactionary and won't do anyone any good. Don't assume that because on one day she expresses certain reservations, discomforts, irritations, or annoyances with how the relationship is, that it's a death knell for your marriage. Everyone hits bumps in the road, nothing can be hunky-dory all the time, relationships and marriages are imperfect.
Now, it may be that she is not handling her NRE well, and if poly is to work guidelines must be established and adhered to, but I don't believe that taking a divorce as the next step will really help anything. All it will do is mean that you won't have to listen to her anymore, and you will pay lawyers lots and lots of money for that. I think finding a counselor and going together is the best step. It sounds like communication is an issue between you, she is coming out with all this stuff and perhaps not expressing herself in the most caring way, and when you feel shut down by her, you back away without fighting hard enough for your side. A third party could help. Please try that route before seriously considering separation or divorce. I tell you this as someone in the midst of divorce right now -- it takes an extremely heavy toll on a couple, and I don't even have kids, which would exacerbate the devastation.