On one of Team Seven’s earliest ninja-in-training missions in Naruto, they are tasked to protect the bridgemaker Mr. Tazuna who, unbeknownst to the group, fears he will be attacked on his journey back to the Land of the Waves by the sinister Gatō’s hired thugs. While Naruto, Sasuke, Sakura and Kakashi manage to defend themselves and their client from Zabuza and his partner Haku, it’s not long before they meet again.
On the outskirts of the village where Team Seven are recuperating, Naruto decides it's time to test his growing skills. In the process of his training, he overdoes it and falls unconscious in the forest where Haku is gathering herbs to heal Zabuza. While Haku has every opportunity to take out the unsuspecting ninja, he decides to spare Naruto's life and talk to him instead. This left some fans confused at Haku's decision - here’s why he ultimately let Naruto live.
To understand Haku's decision, it's important to know his backstory. Haku was born in a small village in the Land of Water. His mother possessed and passed down the Kekkei Genkai ability, which was greatly feared within the surrounding area as descendants of this bloodline were often used as mercenaries in the Third Great Ninja War. The memories of these terrible battles and the people who had lost their lives caused many to have a deep-seated hatred for anyone holding this ability.
With this knowledge, Haku’s mother decided not to inform her husband about the Kekkei Genkai -- or that her son had inherited it. When Haku was finally able to use his abilities, he would proudly show his mother. However, she scolded him for this, fearing that people within the village would harm both of them if they were discovered. Unbeknownst to them, Haku’s father saw this act and, in a state of fear, murdered his wife and then intended to do the same to his son; however, Haku defended himself and killed his father in the process.
Now orphaned, Haku took to the streets and was forced to survive through eating scraps of food from the trash. The rogue Zabuza happened across Haku and, taking pity on the young child, offered to train him in the ways of the shinobi. From this moment on, Haku dedicated his life to Zabuza and the goal of becoming his perfect “weapon”.
However, Haku was never the killing machine he believed himself to be. Instead, he disliked his need to kill others in battle and the role he played as a tool in his master's armory. Although Haku was incredibly loyal to Zabuza, and in many ways loved him as a father, he did his bidding out of respect for saving his life and an extreme lack of confidence.
Upon finding Naruto unconscious in the forest -- having overdone it with his training once again -- Haku does momentarily consider killing him. However, just as he is about to make his move he decides to wake him up. While Zabuza’s influence initially took control over Haku, his inner non-violent nature won over and allowed him to take charge of his emotions.
Haku’s disturbing childhood no doubt had a major part in this decision and the continued consideration he had for the young shinobi. While only a few years separated the two, Haku likely despised the idea of harming such a young person. Furthermore, killing Naruto in this fashion would've only confirmed the fear his father had of his bloodline, who were associated with assassins that killed in this very manner. To fight openly and with honor is likely a virtue Haku valued, and to renounce this ideal for a small tactical advantage just wouldn’t make sense.
When Naruto and the gang's final battle against Zabuza and Haku takes place, Haku’s distaste for death becomes clear when he requests to fight the young shinobi rather than his master, Kakashi. While Zabuza accepts this, he acknowledges that Haku's desire to do so stems from his wish to save Naruto and Sasuke. This is confirmed when he throws his needles into von-vital areas when battling them, showing that his goal is to subdue rather than destroy. After all, as Kakashi points out to the rest of Team Seven, Haku’s weapon of choice (Senbon) has a “low ability to kill”.
While killing was not the favored option for Haku, he would do anything to protect his master. Although Naruto might not have been considered a threat, Kakashi certainly was. Had he been in the same position as Naruto, it is possible that events would have played out differently.