Hi DK.
It is great to hear that you have improved things for yourself so much!
Healing, recovery, whatever you call it, is not linear that's for sure. I find that even when I feel like i have fallen back, I am still ahead of where I was the last time I was there (does that even make sense? )
I suppose the answer to your question is I really want her to continue the help she is receiving and live her life with myself and our children but in the meantime I have told her in no uncertain terms that I will not be a doormat whilst she swans off with anyone she may desire.I hope she understands how much I love her but I have to protect myself and my children in the process
This sounds right to me. You do have to protect you and your kids. You can learn to communicate boundaries without being a doormat while also learning how to consider your wife's needs and sensitivities as well. I am not saying this will fix your relationship but the tools we offer here can help a great deal especially because you have contact due to your children.
Have you ever read the following workshop we have?
The Do's and Don'ts of a BPD Relationship It helps you see what it takes to have a relationship with someone with BPD and gives a glimpse of what you will have to do in terms of any changes you might have to make.