Why are pilots deemed unfit to fly after emergency ejection?
Ejection Seats are not a free ticket out. They are incredibly violent and rough on your body. This newspaper article has a more chilling quote from an interview: 


  About one in three will get a spinal facture, due to the force when the seat is ejected - the gravitational force is 14 to 16 times normal gravity and it might be applied at 200G per second. Bruising and abrasions are typical from the shock of the chute opening or the air blast. In the early days, there were cases where pilots would eject into very-high-speed air and it would whip their arms behind and break them, pop their shoulders out; same thing could happen to the legs. Source


Hence, it is very possible to get back pains and a host of other problems as a result of ejecting. Since these type of things are not that easily reversible, you'd rather take the safe path and remove then from the cockpit than put then back in a work environment that known is pretty hard on your body. Aircrew seem to agree:


  “It was the most violent thing I’ve ever felt in my life,” says one of the B-1 crew members, whom the Air Force asked me to identify as “Captain IROC.” “I lost a full inch in height,” because his spine absorbed such tremendous G-forces. Source


Modern ejection seats are however increasingly intelligent and will gauge the ejection force applied to the conditions, cutting down the number of serious cases. 

This paper discusses the symptoms of four individuals who crashed their jets in mid-air. The medical problems encountered with ejection can be classified as follows:


  
  Injuries from the emergency that causes ejection—fire or collision.
  Canopy jettison: burns from “MDC splatter” and cuts from fragmented plastic. For these reasons, aircrew are always advised to wear their visors down, to protect the face.
  Firing of ejection gun: spinal injuries.
  Entering airflow: wind blast may cause lung damage; seat tumbles at variable speed, which may be as high as 180 rpm. (All seats have a drogue parachute or deployable aerodynamic panels to prevent tumbling); flail injuries to extremities.
  Parachute deployment: snatch injuries.
  Landing: lower limb injuries.