First of all, let me say that your son's attitude is a very good sign. Teenagers often engage in very black-or-white thinking, with little tolerance for anything in between. The only thing that will break them out of this is real world experience. It is excellent that he cares about doing the right thing.
Second, get some good firsthand historical accounts. Let him read for himself what leaders of rebellions were thinking when they led their rebellions. He will quickly learn that many of them were actually defending the law as they understood it against "legal authorities" who were blatantly violating the law. Sometimes they won, sometimes they lost, sometimes they had good ideas, sometimes they had bad ideas; but they all recognized that authorities could persist in doing bad things, and that sometimes the people had to act against such authorities.
Personally I like first or secondhand accounts of the American Revolution (but not the superficial overviews typically called "history books") - the sort either writing about their own experiences or the author writing directly from the participants' notes with frequent quotations, especially if written in the immediate aftermath. I like this period particularly because there were so many well-educated and literate people commenting on why they were doing what they were doing. Of course, many of the sons of those revolutionaries sadly failed in the third war for American independence, but many of them also recorded their opinions. (And Clyde Wilson's recent short book of essays, "The Yankee Problem", gives some good insights into the origins of that conflict.)
But accounts from many periods and places are similar. The one book I recommend to everyone is David Livingstone's "Missionary Travels and Researches in South Africa", because Livingstone was in a unique position to be a qualified proto-anthropologist who was also the first European to contact, and write about, numerous tribes in the middle of Africa who had essentially no contact, even indirectly, with European culture prior to Livingstone's arrival. Livingstone himself already spoke the language of one of the chief tribes in the area, having previously spent years with a related tribe that spoke the same language. His account gives a sympathetic but realistic view of humanity without the influences of the modern world, and personally I think it should be required reading for anyone in the humanities.
But that said I also particularly recall reading about Axum (or Aksum) and the Axumite empire; Schiller's account of The Thirty Years War in Germany, and R. B. Cunninghame Graham's accounts of the history of Paraguay, including the Jesuit Wars and the War of the Triple Alliance which was the most devastating war in modern history. Despite his socialist leanings (somewhat forgivable seeing as the full horrors of socialism were not well understood at the time - and illustrated in "A Vanished Arcadia" which was supposed to demonstrate how socialism could work but really only showed that when Guarani Indians, a relatively advanced tribe, were forced into political associations by external threats and placed under the leadership of some of the most intelligent and capable men from all of Europe, they could sort of manage to get by on a small scale as long as they adopted some capitalist principles, but not so well that they didn't all leave every time the external threat receded) he was an excellent writer and historian. (Cunninghame Graham was also a friend of the author Joseph Conrad, and several of Conrad's most famous characters are based on him.)
Incidentally, the books mentioned above by Livingstone, Schiller, and Cunninghame Graham are available free from Project Gutenberg. I would also recommend the biographies of Francis Marion available there, particularly the ones by Simms and James. (The Weems hagiography of Marion is useful primarily as a demonstration that books are not always to be trusted. Weems, who famously told a lie about George Washington never telling a lie, was well known for his fabrications.) I know about these books because I put them them online in the 1990s. You should also be able to find an excellent book about Aksum by Dr. Stuart C. Munro-Hay, via Google.