The most obvious interpretation of the novel is that it represents the death of a bygone era, both the good people who will be mischaracterized by history, and of the evil people who contain more vileness and hatred than most care to admit. This novel even includes a blatant act of terrorism against a black young man. Unfortunately, the death of this era did not mean the death of racism, and unfortunately, many of the novel's core lessons are still lessons that people need to learn today. These lessons ultimately culminate into a single bit of wisdom: Everyone dies, so let's treat each other equally.
These two sentences may seem like a non sequitur, but they are absolutely not, in the context of the story. In a sense, the reason Sherman Pew dies is because the Judge is spared from death (even though his health is seriously in turmoil), and so his hateful leadership of the town still exists. But when eventually he dies, maybe his legacy of racism continues on, but for how long? There's a sense in which the death of true American racism—not that racism is gone from today's society, but there is a sense in which today's racial reconciliation involves dealing with the past ages of blatant hatred. So even the forces of evil must come to an end eventually, because all evil men die. Unfortunately for Malone, that also means that all good men must die too, but his reward is that he dies honorably in the arms of his loving wife. The judge will die in the shadow of his evil life on earth, disgraced in history.
There is another important meaning of the title, Clock Without Hands. It seems to be a remembrance of Ecclesiastical wisdom, with the central idea being that death is the end of every person's life, whether good or bad. There is a question posed by the plot: Why be Malone instead of being the judge? The answer is implied by the mysterious nature of death—since all men are equal in death, all men are equal in life, especially with the risk of Christian judgment (which was a given in the South at this time).