I too struggle with the concept of the covenant was not there. I made the commitment and the covenant with my vows. It is a marriage. We were not saved when we got married, that happened 8 years later. There is so much in my wife's behavior, responses and attitudes on life that do not align with God and being saved. I do not know how to wrap my mind around that. I think the only correct biblical approach is to legally separate. That being said, my wife will likely push to just divorce. If she changes the goal to divorce, then it is not me that is pursuing the divorce. I feel that falls in the unequally yoked aspect. That does not make it right, but I feel that I am honoring God, as best I can in the situation.
My patience and tolerance for really bad behavior is waning.
I went through the exact same thing- my wife left and stated that she'd divorce me as soon as she legally could (1 year). I fought that for months and did everything possible to reconcile, but now I'm at the point where I have to give it to God. If her heart doesn't change, that is God telling me something.
In your case, why do you want to separate? Really think about that because you've said multiple times, if you separate, she'll file for divorce. Don't let your perception of what she might do influence what you'll do. Trust in God.
Yesterday was really tough for me and my wife was on my mind almost the entire day. Then I woke up this morning thinking about how we could talk this out and fix everything if she'd just be an adult. But that's doing the same thing you're doing, trying to predict what would happen and playing the "what if" game.
God doesn't do "what ifs", He has a plan for all of us and it doesn't include spousal abuse. Do everything you can to work thru things while at home but if you need to step away for a bit, it has to be for you and no other reason. Trust in your faith regardless though and keep praying for guidance. It will come...or maybe it's already there but you're not ready to receive it.