If the school is quite flexible, I'd lean toward accelerating all the classes necessary to be a good fit, but not accelerating on the books. I would look at how many classes the school offers for when your DS gets to high school -- will they be able to accommodate his progression? Do they have AP or similar classes and dual enrollment options with colleges? How high to they go in math/science? If they have enough variety in the higher level classes, you might be able to squeeze another year out of the school without the double skip.
Then again, graduating at 16 isn't so bad. I took my last high school classes at age 16, and spent my senior year as a freshly turned 17yo at the local university through our state's post-secondary enrollment program. It was fine. Depends on the kid.
