I think it was a fair call on the penalty. Benatia came in with heavy hands on Vazquez's back and played his left leg across Vazquez's chest as the ball came in - all of which knocked him down. It's one of those classic questions of whether the rules don't apply in the final moments of a game. At that point, with that play, it's a penalty. It wasn't egregious or anything, but I think the contact was enough to be a foul.
If you look closely at Buffon's interaction with the official, it looks like he grabs him by the waist to turn him toward Buffon so that he could yell at him. I think that touching is what angered the ref and he pulled the red. I think you're right that the ref has to be able to take a certain degree of yelling at a huge call like that - but they do draw the line at players grabbing them.