Although there was minimal to no disturbance inside the drip-line, the monterey pine at the turn point started declining after the drainage project of 1996. One could speculate it would not have survived the pitch canker or turpentine beetle anyway.
Regarding the reshaping of the fairway: grades were changed to enhance surface drainage throughout the fairway and rough. Overall the biggest grade changes were to the left side of the turn point out into the rough (i.e., the slight mound on the left edge of the fairway.
From the approach through the green were where the significant changes took place. The green area increased by about 50% and the approach linked up with the fairway. Also, the median elevation of the green was about 6-8 inches lower than before. If memory serves, the approach was previously short, almost like a false front, being the swale was constantly wet.
With hindsight, I think the hole would have kept it's teeth if the green was left alone or rebuilt to it's original size.
In addition, if one were to look back at Spy from 1966 to present, you would see changes throughout it's short history. Bunkers altered or added, greens reduced in size, tees added or moved, etc.
And if you really want to go deep, look at the routing from 1965 (when it was called The Pines). The course was much longer (almost 7000 yds.) and there were bunkers in locations much different than the "original." I once heard the story that RTJ had the first tee where 18 green now sits and the routing was basically reversed from the present routing.