Perhaps there is a threat that Kakashi has detected, and he believes the best way to keep Naruto safe is to take him out of the village. It could be a group or an individual who is specifically targeting Naruto within the village, and by leaving, they can avoid this danger and also work on finding a solution to deal with the threat on their own terms.
It could also be that Kakashi wants Naruto to gain a broader perspective. In the village, Naruto is mostly surrounded by the same people and the same ideas. By taking him out, he can expose Naruto to different cultures, ninja techniques from other regions, and different ways of thinking. This will not only make Naruto a better ninja but also a more well - rounded person.