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His feelings change quite a bit throughout the course of the novel. At the beginning, he is mildly amused by Leper and all of his nerdish ways; he tolerates Leper, is kind to him to a certain degree, and even defends him against bullying on occasion. He feels sorry for Leper because he is such a nerd, and pities him.
Later, after he visits Leper after Leper is released from training camp, he first feels pity and sorrow at Leper's predicament. But, that is soon replaced by fear and repugnance. He fears the way Leper is behaving, is terrified of the accusations Leper is making, and even hates him a little bit as he leaves. It is a hatred born of his own hatred for himself; Leper reminds him of what he did to Finny, and that makes him angry. Gene doesn't want to think about it, and dislikes Leper for reminding him. He also resents Leper's clinginess and desperate need for his friendship; it is pretty intense, frightening, and pathetic in his eyes. He also fears Leper because he is an ugly and unwelcome picture of what war can do to a person.
At the end of the novel, his hatred crystallizes as Leper reveals the true events of the tree incident; however, Gene is so wrapped up in Finny's next accident that there is no time to dwell on it. He moves on. Leper is just a side-tale in the main tragedy of Finny's demise.