Naruto's character could develop in a more complex way. Killing is not something he takes lightly, so he might struggle with guilt afterwards. This could make him more somber and less naive. For instance, he might question his own values and what it means to protect the village.
He might become more isolated as a result of killing Root members. The village might not fully understand his actions, and he could be seen as a bit of a renegade. However, this could also strengthen his resolve to do what he believes is right, regardless of public opinion.