Young Hannibal is held prisoner in his family's hunting lodge by opportunistic war criminals
who have murdered the rest of the Lecter family and servants leaving
only his young sister Mischa and Hannibal alive. After eating a
scrounging for food (including a rotten squirrel) and only finding scrawny hens to eat raw, the men take Mischa by force and prepare her for consumption in her own copper bathtub. Not only does Hannibal
witness this horrific act but he unwittingly partakes of his sibling
via sips of broth made from her bones proffered by one of the men
called "Pot Watcher." Thus is the genesis of Hannibal the Cannibal.
One might call this the "inciting incident" in Hannibal's career as cannibal and criminal, though. No one act is enough to turn a man into a sociopath, and Hannibal as he is realized is unlikely to have become a serial killer -- the reinforcement that the rigor of a successful foray in medicine would provide almost entirely precludes it. Most serial killers, distinguished from "people who kill, or even kill a lot," feel almost entirely worthless, except when they are brutalizing or killing.
No, what's at stake here is Harris's fantasy construct and our fascination with him, and for a greater understanding of Hannibal's motives, we must go to the books. Hannibal has an amusing contempt for God: his blasphemous Christ watch in Silence, his collecting of church collapses, his statement that "Typhoid and swans came from the same God," which is also a deleted scene in Silence. We learn of the inciting incident of Mischa in Hannibal, about which Harris writes, in the thoughts of Hannibal, "His modest predations paled beside those of God, who is irony matchless, and in wanton malice without measure."
Ashkenazi Jew Hannibal Lecter lost his God in the snow during the war, and later ponders to Lady Murasaki whether God meant to eat Isaac after Abraham sacrificed him. (This paradox of God's cruelty is also explored to some extent in "The Believer" with Ryan Gosling.) And Hannibal says in the book Silence, after Agent Starling suggests that he take the VICAP test so that he might find out what happened to him (to make him a killer), "Nothing happened to me. I happened. You can't reduce me to a set of influences. You've given up good and evil for behaviorism... Can you stand to say I'm evil?"
Lecter also survived the brutal bullying of his childhood, a common thread in the history of serial killers, and he takes to killing and eating his captors as revenge some years later. After that's over, then what? Why does he kill? Because he wants to. In the moral framework of the novels, he kills because people are rude, and "discourtesy is unspeakably ugly to me." (See Mason Verger, a deer hunter). Then again, he kills and eats Benjamin Raspail because Raspail doesn't play the flute very well (Benjamin Raspail is a victim of Buffalo Bill in Silence, ostensibly to simplify the narrative, I'm sure). He is a sociopath, reduced by his impulses to an addictive pleasure seeker, and killing satisfies him. By eating his victims, he mocks the God who left him and his sister to die. So he's not entirely an atheist, one supposes, if his actions are meant to defy God.