I'll be honest with you. I'm not sure why this is turning into such a big deal is to everyone. I'm not saying I don't understand the mechanics of the change. And I do see the impact to us Hunters, especially endgame raiding Marksman Hunters. But really, let's take a step back and look at the reasoning behind the change.
Ghostcrawler said that they implemented this change after noticing everyone was picking up Armor Pen at the expense of their core stats. Really? And somehow we're surprised that when a secondary stat becomes more important than a class' primary stat and it forced a nerf? It seems more of a correction in my opinion.
If you're a raiding Marks or Survival Hunter you should be focusing on picking up as much Agility (Attack Power if you're a Beast Master) as possible. Hence why in Cataclysm we're seeing things like Armor Penetration removed from the itemization.