In my experience, the neck wood gives the most impact when it comes to a guitar's tone, especially if it is a neckthru. Chances are, even if silver maple isn't a good tone wood, it won't make much of a difference in a neckthru. That's just my opinion based on my observations.
BTW, I hope the saw mill you are getting your wood from has a kiln, or the wood has been sufficiently air-dried. Otherwise, you will have to dry it yourself (IIRC, 1 year per inch of wood thickness).