Rewatching the scene, I think that what sealed the deal to the ref was the fact that Stephens laid his face on the canvas instead of trying to protect his head. Also what made him turtle up was another shot to the same region that made him wince in pain and collapse to the mat. Can't complain about a bad stoppage after sending so many signs that you might be in trouble.
This stoppage made me recall the stoppage in Mendes vs McGregor. An exhausted Mendes collapses to the ground and turtles up seconds before the end of the round. McGregor lands a few shots on Mendes' arms and the judge stops the fight.
Personally, I believe that if a fighter is turtled up, it's fair game for the ref to stop the fight. Turtling up is taking advantage of the rules not to absorb damage in a position that is extremely vulnerable in a real fight.