Is there anyway to disable clients GameObject instance from Server or Vice-versa?

do u mean that the object is instantiated only on client-side and not the server (not Network.Instantiate), then if that is the case then u need to attach a networkView to the g.o that u want to disable and then from the server side just access this g.o by any method u like and disable it , e.g

 // server-side
 GameObject.FindGameObjectWithTag("goName").networkView.RPC("Disable", client);

and the code on client-side may look like this :

 // client-side script attached to the object that we want to disable
 [RPC]
 void Disable(NetworkMessageInfo msg)
 {
    gameObject.SetActive(false);
 }

and u can just do it from the client to the server. it should work properly hope that help