An intelligent defense means, at the very least, the fighter must be looking to escape the position instead of just "weather the storm." If the guy's not even showing that he's looking for a way out, then it's hard to justify an "intelligent defense."
He could've been completely out, like Schaub, just staring at the lights. Instead, he tried to minimize some of the damage by covering, but he made no attempt to control
That's a crappy defense.
If the nose is going to be the reason to end the fight, the referee can't make that decision. The medical professional has to be the one to make that call on behalf of the fighter.
Hamill's reason for why he couldn't continue was the one that ended the fight. It's the only one that matters when it comes to reevaluating the call by Mazzagatti, because it is what lead directly to the end of the fight.
If Mazzagatti had actually done his job (stop the fight, wait for input for the doctors before issuing either a deduction or a DQ), there might be some room to defend his actions, but I think it's clear that if Hamill had just suffered the nose injury, he probably could've continued fighting. We've all seen worse in terms of blood (Josh Haynes, Edwin Dewees, and so on) and open cuts, and fighters have worked through those.
The dislocated shoulder is a fight ender. It was for Manny Gamburyan on the TUF 5 finale, it was for Xande Ribeiro in Absoluto at Abu Dhabi this year. It is always a fight ender, because it is impossible to mount a sufficient defense or offense when lifting your arm is that painful.
Just point of fact, the referee is fully vested to make the determination whether a fighter is able to continue, no doctor is required for that. He may, if he wishes, call the doctor in to evaluate the injury but that is not required to stop a fight (or deduct a point or DQ).