One way is to use the 9/11 event as a backdrop to explore deeper themes in the Naruto universe. For instance, the idea of unity in the face of tragedy. The Hidden Leaf Village has faced many threats, and just like how the world came together after 9/11, the village can show similar unity. It can also explore the idea of how different cultures (in the Naruto world) can come together in difficult times, much like different countries did after 9/11.
To blend the two without disrespect, it can be more about the emotional and philosophical parallels. The shock and grief that followed 9/11 can be compared to how the characters in Naruto feel when they lose comrades or face a great disaster. And then, the hope and rebuilding that came after 9/11 can be paralleled with how the characters in Naruto strive to make their world better after a great conflict.