In A Separate Peace," the narrator returns to the scene of the crime, so to speak, years after the events that he relates to the reader in the novel take place. The statement you ask about refers to the narrator's reaction to those events.
The tree is only a tree, when Gene returns and sees it again. The associations and mythical-like qualities the tree held for him those years ago are no longer present for him. The tree is no longer threatening or "bigger than life." Also, he did not despair over what he did to Finny. He has learned to live with it. And his love for Finny was very much envy and jealousy and obsessive suspicion. Gene's statement is a sophisticated response, in that he doesn't try to explain away what he's done, or try to give some moralistic one-liner to demonstrate some lesson in all this: he doesn't try to assign some cosmic significance to the events.
Time has passed and nothing lasts. Life continues. Gene has moved on, as, of course, we might assume other characters have--except Finny.
My answer might be off the track, the phrase is a very good example of reality.
- Violence will leave permanent damage. And creates negativity that oppose (eg.love, tree, death)
Then violence could generate hatred to counteract love, destruction to trees, and futuristic malice, regret that lingers forever.
Violence is the ultimate destroyer of things. It creates a cycle of causality.