Was it right to look at the subject from the perspective of a young, naïve boy in John Boyne's novel The Boy in Striped Pajamas?

Whether or not it was "right" to tell this story with a young boy as the focus is really a matter of opinion, so I cannot answer that question for you. However, I do think that The Boy in the Striped Pajamas ("Pyjamas" in the UK) makes an important point and does it very well. So much of history seems to belong solely to adults. Children are often left out of historical documents and accounts, and so are often left out of historical fiction as well. The truth is that there were children involved in the Holocaust, and entire families were shaken up by the events on all sides. 

The protagonist, Bruno, is a powerful character because he is rather oblivious (as most children are) to what his parents do and what the strange place beyond his fence really is. He has just moved to a new home and naturally is in want of friendship, so when he meets Shmuel, he makes good effort to befriend him. Shmuel and Bruno are mirrors of each other, sharing the same birthday, but they live very different lives on their respective sides of the fence. This character dynamic shows a stark contrast between the lives of those who benefited under the Nazi regime and those who were punished. It is all the more powerful for telling a story about those who are often left out of our discussions of history-- children.

Bruno and Shmuel have all of the curiosity, love, and confusion childhood offers. Their story is one of the commonplace but undiscussed circumstances such trusting and adventurous children were forced into during the time of the Holocaust.