You are effectively making one of my points... that after Pryor hit him like that, there was no way to prevent Favre's head from getting hit due to "post contact physics".
If that's true, then: hit him differently. Don't hit him like that.
The point of the fine is to alter tackling behavior so injuries like Favre's don't happen.
Have you actually played the game? This game moves faster than you can likely imagine, so your apparent perception that defenders will crunch trajectory physics faster than NASA probably needs to be considered unrealistic.
There is also no rule that says "don't hit in the head" as you apparently interpret it. The rule I expect you are invoking likely
says "using any part of a player’s helmet (including the top/crown and forehead/“hairline” parts) or facemask to butt, spear, or ram an opponent violently or unnecessarily; although such violent or unnecessary use of the helmet and facemask is impermissible against any opponent, game officials will give special attention in administering this rule to protecting those players who are in virtually defenseless postures (e.g., a player in the act of or just after throwing a pass, a receiver catching or attempting to catch a pass, a runner already in the grasp of a tackler, a kickoff or punt returner attempting to field a kick in the air, or a player on the ground at the end of a play). All players in virtually defenseless postures are protected by the same prohibitions against use of the helmet and facemask that are described in the roughing-the-passer rules (see Article 12, subsection 3 below of this Rule 12, Section 2)."
If a player's body, as a consequence of a hit, strikes the defender's helmet, how is the defender "using" his helmet? "Using" implies action, not inaction (specifically the action of the tackled player's body on a helmet directed elsewhere). Some players bend, some are rigid. Do you expect defenders are skilled mind-readers on how offensive participants will take a hit?