Update, 12/17/13: Yoni Appelbaum, Atlantic contributor and historian extraordinaire, has passed along some of his own fascinating research into the Santa-tracking story. First of all, he wrote in an email,
It turns out that the military, and other government agencies, had been using Santa to sell their missions long before 1954. At the height of the Second World War, Eisenhower’s headquarters put out a release offering 'Christmas guidance' to war correspondents. It confirmed that 'a new North Pole Command has been formed,' that 'Santa Claus is directing operations,' and that 'he has under his command a small army of gnomes.' The censors, though, suppressed the location of Santa’s headquarters, directed that his delivery methods be described only as employing 'secret devices' or 'special scientific techniques,' and proscribed 'any mention of radar or speculation on the purpose of reindeer antennae.'
Which is both weird and delightful (army of gnomes! radar antennae!), and, regardless, suggestive of the fact that CONAD had a vested interest in PR campaigns as well as military ones. It was primed, basically, to take advantage of the good cheer of Christmas for its own ends—among them, promoting its military technology. Which makes sense, and which would help explain why NORAD would have so faithfully continued the tradition year after year.
Yoni has also found, it's worth noting, disparities in the early stories that informed NORAD's, Snopes's, and other current accounts of the intercepted North Pole calls. When Shoup told his story to the LA Times in 1980, he mentioned an unlisted line that a child had accessed. In a later newspaper story, in 1999, Shoup mentioned a much more limited, Red Phone-style line, and multiple children. My retelling originates from the Snopes account of what happened, but I'd love more documentation. If you have access to that, or know anything additional about the original story, drop me an email (mgarber[at]theatlantic.com). And big thanks to Yoni for sharing his research.