Since you are legally married and have not court order in place, then yes your husband can legally take your children for the weekend. If you believe they are in danger with him or he has put them in danger, you need to consider a Child Order of Protection, as well as filing for divorce.
You need to talk to your attorney about why the case was continued, and why only the other party had to be present in court. You have the right to be at every one of your court dates. If your attorney is unable to explain to you what is going on, you need to go to the courthouse and review your court file.
Please be aware that both you and the father have certain rights to your unborn child. However, until you or the father files for Paternity, you will have sole legal and physical custody of your child. The father will have no rights to the child. A paternity action will help determine three things: who is legally the father of your child, set up a parenting plan and decide all financial decisions between you and the father.
In Missouri there are two types of Orders of Protection, Adult and Child. It sounds like you have an Adult Abuse Order of Protection against your ex. You need to read it carefully to determine what it encompasses. You should also call your local police department to see how they will intepret it. It sounds like you need to be exchanging your son at a neutral location such as a police station.