Matt, I re-read your posts, and it's not clear to me whether or not you've vocalized these matters surrounding the girlfriend being at your place too much, or have you just kept your mouth shut and hinted and hoped things would get better, all the while the situation growing more and more untenable for you? Because, you say that the "lines of communication are open", but have you USED them? Have you had a conversation about this, and have your wife and her GF agreed but done what they feel like anyway? Please explain it better so I can understand that.
Also, you have made it clear that you do not want to be in a "poly family" with GF. Does your wife accept that, or does she tell you one thing and behave in another way?
It would be very helpful if wife and/or GF came here to give their sides of he story, before people give you too much more advice based on what you say and what they think might be going on in the other people's minds.