When talking about a novel, "tone" refers to the author's tone, or attitude toward the story he's telling. We don't know about you, but we'd say that Philip Pullman means business. Unlike some fantasy stories that are very lighthearted or even silly, The Golden Compass is serious. Pullman doesn't shy away from weighty issues like betrayal, cruelty, and death – even in a book for tweens and teens.
That leads us to the topic of morality. We'd say that Pullman's tone is also moral because he's very concerned with right vs. wrong. He doesn't always make it easy for us to tell who the good characters are and who the bad ones are, but he does want us to think about it. For example, why is the Master of Jordan College trying to poison Lord Asriel? Is that right or wrong? And what are we to make of Lord Asriel, who doesn't seem all that bad, but then he kills Roger for the sake of his experiment?
We also know that Pullman is concerned with morality because, well, he's said so. Check it out:
"Try as hard as you can, you can't leave out morality from a book. Everything we do, however small, has consequences. The greatest fiction always has a sequence of actions followed by reactions, followed by consequences. […] You can't leave morality out unless your work is so stupid and trivial and so worthless that [nobody] would want to read it anyway." (source)
There you have it, folks.