We puzzled for a while over this one. Who kills the Witch? Will's dad. Who kills Mr. Dark? Will's dad. Who unlocks the secret to defying death at the hands of Evil? Will's dad. (The secret, it turns out, is laughing.) Like you, we noticed a pattern of heroism here that has nothing to do with Will except for his genetics.
Still, we argue that William Halloway is the true protagonist of this story because 1) we see the story primarily through his eyes; 2) he is constantly fighting the good fight with his friend Jim, who is being lured to the dark side; and 3) he is the one inspiring his father to action. Charles Halloway, to put it bluntly, is a sad, depressed, lonesome figure of a man before given the opportunity to combat evil on behalf of his son. As Charles says several times, he believes Will to be "all good." Will's unerring sense of what is good (marbles!) and what is evil (the carnival) serves as a guiding light to his father. And let's not forget Will literally served as a guiding light to his father in Chapter 49 when he strikes matches in the Mirror Maze and helps Charles accept the images staring back.