Serra stated that in 8 professional fights that is the only time he has been beaten up.
It was a good stoppage. 5 round of that and Serra would be in rough shape. Those knees won't knock you out, won't cut you open, and would make your face deformed. Those knees will break ribs and possibly injure organs.
The ref knew Serra was taking a beating and wasn't defending himself. Going into the turtle position isn't defense, its survival.