I really don't think Blizzard will abandon the turn-in system entirely-- although Badges are a little different than they've ever done it before (and yes, they probably do need a little tweaking in how they're given out), the system works. It gives people a reason to run instances, and it lets you choose what you want to run, and then choose the loot that you want from that run. Token-based loot, in general, is so far a great alternative to the drop or the quest system.
However, I can definitely see Blizzard moving on to some new tokens. Maybe as WotLK comes out, they'll just spread these Badges around more and more, making the Heroic loot more and more easy to get, and then when we reach Northrend, the next iteration of token loot will go back to being much more rare.