You want to break up with your GF in your tier of the relationship, which is fine... You don't want to limit her relationship with your wife, which is fine...
Take a breath and recoup. Have this talk with her - that you can't be in a relationship with her anymore, but you don't want to jeopardize what she and your wife have. Take that step first, and then talk with her and your wife about how much time at your house works for you. It's not unreasonable for you to want to be around her less after breaking up - in fact, it seems like a reasonable outcome of breaking up.
You've had the ability (or the curse?) to think about this ad nauseum, while she has no idea this is coming. Taking it one thing at a time and letting the "less shared time" be an effect of the breakup may help her feel less like she's getting hit by a truck.
Good luck to you all!