What is the "pie" in "Cutie Pie"?
Solution 1:
The term seems to be in use before Nicholas Fisk wrote his story so it may be that he popularized the term rather than coining it. The earliest reference I could dig up was a pony named "Cutie Pie" who won a modest sum in a show ponies convention in 1919, so it's possible that the term was in use as a diminutive nickname, perhaps to mean something like cute + sweet (as a pie).
The Oxford English Dictionary points out a reference from a year later of a cat called "Cutie Pie" mentioned in the Washington Post. They do not attempt to provide an etymology however, other than to say that "cutie" is a derivative of "cute" and then to point to the phrase "sweetie-pie" as probably related. Like "Cutie Pie" the earliest instances I could find was as the name for a pet (dog in this case) in 1922.
Solution 2:
I don't know what the pie means, but the phrase dates at least to November 28, 1916, as found in The Washington Herald:
(Characters-Harry th' barkeep over th' phone with someone in Washington.)
Someone-Hello! Is 'at you, Harry? Well, say! Listen! Listen, kid! Ain't It no way you can get off Thanksgivin' an' take me over t' see th' football at Georgetown?
Harry-Not a chance, Cutie-Pie! I'm still in th' hands o' my Oculist!