When one party is in jail and a motion is scheduled, some courts will grant temporary custody to the appearing parent and reschedule the motion for a future date (either when the other parent is released from jail or to have that parent appear by phone), but it is up to the individual court. However, I would not assume that she is going to jail since she is only facing a misdemeanor. If she doesn't appear and she is out of jail, the court can grant temporary parenting time and proceed on the motion anyway. It would not look good if she does not participate in the hearings.
Why ask for temporary custody? It would not only be reasonable to seek temporary, but likely permanent change of custody. How much stability can your ex be providing if she is engaging in violent criminal behavior? I would strongly recommend consulting with a local family law attorney to plan your strategy, whether for temporary or permanent custody. AVVO is a great resource for finding an attorney. I wish you all the best.
This comment is designed for general information only, and should not be construed to be formal legal advice nor the formation of a lawyer/client relationship.
You haven't given us any information regarding your contact with your child. Have you had regular parenting time with him? Do you have any criminal history? Those are questions the Court will ask you in determining what is best for your child in this situation. I would strongly suggest you consult with an attorney to discuss any motions that you may want to file.