Difficult Night

I have three boys. My middle son ran away called the cops on my wife for child abuse. Apparently when I was working out of town she would beat the oldest who is disabled. Today I asked her to move out. First she refused, got mad etc. Later I received a text saying she will step away from the immediate situation and the boys and I can consider our short comings and stop blaming her. That in no way she is giving up her rights to parenting and will resume as soon as possible. When she showed up to take things she told me that she will never forgive any of us for this. All these things are bad but I can’t figure out why I am having second thoughts and in a hart beat would beg her to stay but then I think of the boys worry about what happened when I was away at work and how I missed it for so long. So conflicted some words of advice would be helpful.