Hard to say... I don't think a fight should necessarily be stopped because a guy is taking some unanswered shots; not if the guy is giving the thumbs up, maintaining a closed guard, and trying to pull his arm free. However, it's hard to criticize a referee for not letting someone take undue amounts of damage just because he's still conscious, the refs are paid to recognize situations and use their judgment in projecting where they think that situation is going.
It's not exactly a black/white issue; some people have higher pain thresholds, seemingly thicker skulls and maybe don't mind eating a few punches while they wait for a moment to explode or try something.
Joe Rogan made a good point (I thought) during the Velasquez / Rothwell fight too. Big Ben was taking a lot of shots to the head, but he was simultaneously wall walking which was improving his position and the ref stopped the fight. Don't get me wrong; the tide of that fight was not going to change, Rothwell was soundly dominated prior to the stoppage, and would have been soundly dominated had the fight continued. In fact he was warned at the start of the round by the ref that he was not going to be allowed to endure that kind of beating much longer.
I say if the ref is yelling out, repeatedly, for a fighter to improve their position, and the fighter doesn't try, or doesn't manage to improve it, then stop it. The ref warned them, the fighter heard it multiple times; no results = fight over.
It's a tough call. But at the end of the day, does anyone really want to see someone take excessive punishment just because they can? I don't. These guys are in a rough sport, and the average career isn't too long. These guys need to be able to function when they're time is over. They're not going to have the luxury of a pension.