As for how Batman cleared his name, I would think that most people would have the death attributed to the Penguin, especially after Batman aired the recording of him badmouthing everyone.
As for Shreck being the main villian, I still consider The Penguin to be the main villian. Sure, Shreck used the Penguin, but Shreck's using him eventually backfired on him and led to his ultimate demise. Plus, the Penguin was ultimately the biggest and most dangerous threat.
Was Shreck ever in the comics, or was he invented for the movie?