What is the correct course of action for my situation, given that my conscience makes me feel guilty for giving up custody of my son, who is suffering from neglect and wants to live with me, while my family refuses to help me get him back, and my father prevents my siblings from supporting me? Would my acting without consulting them be considered disobedience to my father?

The best interest of the child is the determining factor in custody. Therefore, the person granted custody must be capable of protecting the child. Thus, if the child is being harmed by being with his father, the matter can be referred to the Sharia judge. Your family should help you in this. If they do not, there is no sin upon you in going to the Sharia court. And if your parents object, but their objection has no legitimate Sharia justification, then you are not obligated to obey them. Trying to convince them is better.