A medical robotic system has a robotic arm holding a medical device, and a control system for controlling movement of the arm according to operator manipulation of an input device. If the medical device is being commanded to a state exceeding a limitation by a threshold amount, then the control system disengages control of the medical device by the input device, servos the arm so that it remains in its current state, servos the input device so that it is set at a position such that a force being applied on the input device remains at its current level, requests the operator to lighten hold of the input device, sets a parameter associated with the input device upon detecting such lightened hold so that the medical device is commanded to a different state that does not exceed the limitation, and reengages control of the medical device by the input device.