You stated that they don't take appeals, but maybe it's worth contacting whoever is in charge of the magnet program with your child's WISC scores and 2e status. How far off were his NNAT scores from qualifying? If they are close, maybe there is some wiggle room given that he is 2e as well. It likely also depends on the size of the magnet program. If they are at capacity with tons of kids qualifying, you may not have much luck.
I think it is appropriate (and common) to look at achievement scores as well as ability, but the NNAT2 is a short, non verbal test that doesn't measure all that many areas of ability. There should also be subject specific ability testing, like the OLSAT or cogat.
It's strange that they won't let your child read what he wants to during free reading. We pick out books from the public library and my son takes them to school. His teacher has never said anything about what he chooses to read.
