In my opinion, the most logical reason for her to have killed him is that he was no longer in love with her or he was going to leave for some other reason.
In the story, Emily is kind of dominated by her dad. She can't have any kind of a normal life because of him. He chases off all her hopes for love with that whip.
But now with Homer, she has a chance, and maybe she feels that it is her only chance or her last chance. If he were going to leave her, this chance would be gone. So I think she killed him to prevent that.