Root motion handled by script. How to still use root motion with disabled navmesh agent?

I have this script from one of Unity's tutorials with locomotion for mecanim. Everything works fine and Mecanim is working with NavMeshAgent. The thing is I would like to disable NavMeshAgent from time to time and still use root motion (for example when a character want to sit down on a chair that is an obstacle or it's baked into navmesh).

At this moment, when I disable NavMeshAgent component my animations are played without root motion. Root motion is automatically set to "handled by script" and it just won't use root motion when the NavMeshAgent is disabled.

Do you have an idea how to modify this script so I will still get the root motion from animations even if the NavMeshAgent is disabled?

 using UnityEngine;
     using System.Collections;
     
     public class Agent : MonoBehaviour {
         
         public GameObject            particle;
         protected NavMeshAgent        agent;
         protected Animator            animator;
         
         protected Locomotion locomotion;
         protected Object particleClone;
         
         
         // Use this for initialization
         void Start () {
             agent = GetComponent<NavMeshAgent>();
             agent.updateRotation = false;
             
             animator = GetComponent<Animator>();
             locomotion = new Locomotion(animator);
             
             particleClone = null;
         }
         
         protected void SetDestination()
         {
             // Construct a ray from the current mouse coordinates
             var ray = Camera.main.ScreenPointToRay(Input.mousePosition);
             RaycastHit hit = new RaycastHit();
             if (Physics.Raycast(ray, out hit))
             {
                 if (particleClone != null)
                 {
                     GameObject.Destroy(particleClone);
                     particleClone = null;
                 }
                 
                 // Create a particle if hit
                 Quaternion q = new Quaternion();
                 q.SetLookRotation(hit.normal, Vector3.forward);
                 particleClone = Instantiate(particle, hit.point, q);
                 
                 agent.destination = hit.point;
             }
         }
         
         protected void SetupAgentLocomotion()
         {
             if (AgentDone())
             {
                 locomotion.Do(0, 0);
                 if (particleClone != null)
                 {
                     GameObject.Destroy(particleClone);
                     particleClone = null;
                 }
             }
             else
             {
                 float speed = agent.desiredVelocity.magnitude;
                 
                 Vector3 velocity = Quaternion.Inverse(transform.rotation) * agent.desiredVelocity;
                 
                 float angle = Mathf.Atan2(velocity.x, velocity.z) * 180.0f / 3.14159f;
                 
                 locomotion.Do(speed, angle);
             }
         }
         
         void OnAnimatorMove()
         {
             agent.velocity = animator.deltaPosition / Time.deltaTime;
             transform.rotation = animator.rootRotation;
         }
         
         protected bool AgentDone()
         {
             return !agent.pathPending && AgentStopping();
         }
         
         protected bool AgentStopping()
         {
             return agent.remainingDistance <= agent.stoppingDistance;
         }
         
         // Update is called once per frame
         void Update () 
         {
             if (Input.GetButtonDown ("Fire1")) 
                 SetDestination();
             
             SetupAgentLocomotion();
         }
     }