This depends on the situation the unit is in.
If the unit is on recall status, then it makes sense the Commander is reluctant to allow leave. If the unit is on normal status, then I would not know why the Commander would deny the leave.
While the Commander has a responsibility to ensure the court order is enforced, the Commander is not required to assist the Soldier in meeting their obligation. The Commander’s responsibility begins if the Soldier refuses to comply, not assisting the Soldier to comply.
This Soldier should have a Family Care Plan in place if he is a single Soldier. While not the most convenient option, the Soldier needs to look at having another family member drive his son if need be. Contact the boy’s mother and see if it’s possible for her to fly out and drive his son back to MT. The Soldier may have to fund the trip or a portion of it. The Soldier needs to look at all options and he can inquire through the Commander’s Open Door Policy, why the Commander is denying the leave. Should the Commander not have a legitimate mission requirement to deny the leave, the Soldier can try the Battalion CSM/CDR’s open door policy.