I don't think the stoppage was that bad. When you watch a slow-motion replay, I can see where it looks a little premature.
But watching it live as it happened, I thought it was a decent stoppage, and the first instinct is always the best one. Also, I always pay attention to the fighter's reaction when a stoppage occurs. I didn't see any big protest from Marquez when the ref stepped in. That usually tells me that he was hurt and needed the ref to step in.

If I'm a ref, I'd rather stop a fight 2 or 3 punches too soon than 2 or 3 too late.