Actually, the Broncos won the game...the final score says so. San Diego didn't stop the Broncos on either the 4th down touchdown or the 2-point conversion.
Anyway...the rule is laid out there pretty simple, it isn't up to the referee. The whistle blew to end the play (which may or may not have been a mistake, depending what the official saw and when), and there is nothing that can be done to change that. The whistle blew and that is the end of the play, regardless of what the instant replay shows. So yes, in your example, if a guy takes off down the field and a ref just blows his whistle, the play is dead...period, end of story. It is how the rule reads. There is no exemption for the head official to change the rules on the field of play.
Stuff lke that happens every Sunday, but people only care if it happens in the way it happened yesterday. If that same thing had happened in the 2nd quarter on the Bronco 32 yard line and Denver had gone on to score a touchdown, nobody would care one bit.