On a side note...why did God punish the innocent snake (a creature He created) and not Satan who was responsible for the deception? Poor snake...
Yeah, I've always wondered about this as well. Snakes are actually very cool creatures and tend to be helpful in keeping harmful rodent populations down and mainly just want to be left alone. Because of this story, many snakes are just killed for no reason at all....sad. But then, the whole of creation suffers because of the Fall, not just snakes.
As for why God does such things... I guess we'll have to be satisfied with the answer He gave Job when Job asked "why"... when we can lay the foundations of worlds and enclose seas with doors, cause the dawn to know it's place and bring rain to the land, then we can instruct God as to what He should have done.