VMware actually updated their docs to show the API call to force a delete recently!
https://docs.vmware.com/en/VMware-NSX-Data-Center-for-vSphere/6.4/com.vmware.nsx.troubleshooting.doc...
DELETE /2.0/vdn/controller/{controllerId}?forceRemoval=true
You were pretty close! Just use the parameter and you should be good to go.
