You are looking at a biblical story way too literally.

I would say that this story, like most of the Bible (or at least Genesis) is a a collection of metaphorical stories and legends that do not correspond with real events but have imagery and symbolism that have value for mankind. Adam and Eve, the naked, perfect and innocent man and woman from that are our ancestors, are a beautiful and emotionally charged story... I'd leave it at that.

However, if you want to believe that the story has some historical basis, you must think about it through the lens of evolution, and interpret it as follows: Adam and Eve represent the species that has not yet reached self awareness. They are happy in their lack of knowledge, and the world is perfect (or at least, in balance). After 'eating from the tree of knowledge' the humans become aware of their nudity, leave the garden of Eden (in reality, our ancestors have left the jungles of the Congo for the harsh savanna). Of course, when the story is seen like this, the incest problem is gone; we are talking about the evolution of an entire species, not just two people. They could breed with other apes, as well as other early humans.