It's your guitar. You are "allowed" do do anything you want with it. You won't be able to get a solid maple neck from Fender, that is true, but if you don't mind after-market products (on a M-I-M strat, I personally wouldn't worry about it), you can get a Warmoth, Mighty-Mite or other strat-style neck. Just make sure it has the same number of frets and is the same scale length.
If you don't know what you are doing, I recommend finding a local guitar-repair shop and see if they'd do it for you. You need to be comfortable with adjusting your truss-rod, basic set-up (action and intonation), and adjusting the bridge string radius to match the radius of the neck. You'll probably want to put a better nut on the new neck too, because if I remember correctly, the nuts that come with those after-market parts are plastic, plus, they have no idea what string gauge you use.
All in all, if you want to do it right, it would be expensive. There would not be a tremendous difference in sound, and possibly not even a noticeable difference.
What about the maple neck do you like as opposed to a rosewood fretboard?
