She can leave all she wants. She can't leave with the kids.
Should she leave with the kids, you file an emergency motion in court for the children to be returned to the matrimonial home. Be prepared for her to return as well and not be happy about it. Buy a digital voice recorder and keep it on and recording the whole time you're in the house or in her presense outside the house. This is hopefully protect you from a false DV charge (false DV is the fastest way for her to get you out of the house with a restraining order and cause you to be at her mercy when it comes to seeing your kids).
I would personally move all your personal items to a separate storage that she doesn't have access to. This will help ensure they don't go "missing" later.
But should she leave with the kids you file a motion for the kids to be returned home and interm custody. It would probably be best if you had a lawyer to help with it.