As long as you are under the same roof, she will be having all the benefits of a marriage and loving husband,while still living the single life, basically for her it will be like living at her parents, if something goes wrong or she needs something her parent/husband will fix it, do it , pay for it. I think if this condition goes on for to long the resentment you will build up will be so great it will always weigh on your relationship. Even if you don't feel up to telling/forcing her to move out yet, you should probably bring it up during your session. Asking the counselor how you should tell the kids shes moving out, making it clear the truth is important(mom doesn't love daddy).
And lightswitch, Making and enforcing boundaries/rules/laws does not make someone a tyrant as long as the rules are not tyrannical, of course she may think they are anyway. You should set a time line or a set of conditions on when the split will occur. And to no one in particular, whenever someone talks about putting it in gods hands I always think about the drowning man joke.
