You have asked two questions so I will only respond to the first. You always need to be wary of reading any novel as an allegory. A simple allegorical reading can lead you to miss some of the depth of the novel. However, your question does point towards the central theme of the novel and how the relationship between Finny and Gene demonstrates it.
Gene appears to represent qualities of envy, jealousy and the ability to commit evil acts. He is so insecure in his relationship with Finny and cannot understand or accept Finny's innocence and naivety. He spends most of the novel silently envious of Finny's natural athletic ability, self-confidence and handsomeness and assumes Finny likewise envies Gene. He cannot understand how Finny does not want the glory that goes with his achievements, such as breaking the swimming record. It is when Finny encourages Gene to study instead of going to the "Suicide Society" that Gene realises that Finny has always innocently loved his best friend without envy or rancour. It is this knowledge of his own suspicion and evil that drives Gene to knock Finny out of the tree.
Finny's innocence on the other hand is established throughout the novel. He only appears to be able to acknowledge a small part of the evil and horror of the world, rejecting the rest. This is why he finds it so hard to suspect Gene and also we see this characteristic in his stubborn refusal to accept that the War exists. Thus Finny can be said to represent innocence and naivety, whilst Gene can be said to represent more wordly and (sinful) human emotions.