Mike,
The short version of your post is "Should we contour greens like the old days to defend par at the green."
The short answer is probably no. I agree with Pat Mucci - I don't think JN introduced the aerial game, I think with his skill, he just refined it and executed it better than anyone else. Good players were trying to do what he did long before, but his strength allowed him to do it better.
I also wonder about the premise of longer green turf helping stop roll. Frankly, I think new balls and equipment more than make up for that in extra spin and its probably easier to stop shots now than before, which would suggest limiting front to back slope. For that matter, downhill putts on fast greens at about 2% are probably scarier now than downhill putts at 6% in the old days. So, it all evens out.
My experience is that greens sloping upwards at 1.33% or more will stop a long iron for most players. Putting in too much slope merely creates a situation where the Pros try to hit a lower spin shot. In that sense, there may be more chance to go past the pin, but they would probably adjust somehow, perhaps putting tee shot strategy of playing to the side that opens the front of the green back in play more.
Distance control is so good at the Tour level now, and so poor at other levels, that "punishing" a long hit by a good player would probably create 4X problems, as well as be experienced 4X as many times by the rest of us. I usually try to accomplish what you are talking about on one (maybe two) pin positions per green using ridges or contour spikes encroaching from the edge of the green. Should a player come up short, that ridge will kick his ball back or shoot it forward. That may encourage some to play pin high, but towards the middle of the green, which would usually leave a mid length putt, so that their birdie chances go down dramatically.
I still think the total slope at a cup location can be near 3%, and not the sub 2% some guys use nowadays, so I guess I do like your theory somewhat. (BTW, the Masters and US Opens use a max cup location of about 4% on very fast greens. And, while they are faster than normal greens, they are also aimed at better than normal putters for one week only, so I think the 3% max is a good compromise)
But, as Colt said, "No putt should run from the putter blade like a swine posessed by the devil." While I have been contouring my greens greatly as a few can attest, I have not found that golfers like them, and have reverted to flatter greens in current designs.