After doing some digging, it seems there's no aftermarket cooler available. You're correct in saying that the problem is that there's a big fat HSI chip where the GPU would usually be, and the GPU itself is down the back of the card.

"The following nVidia graphics cards have no solution - 7800GS (AGP) and 6800GS"

Application:
ATI:
X1950, X1900 series
X1800 series
nVIDIA:
7950, 7900 series
7800, 6800 series (except 7X00 GS AGP)

Mounting holes on 7xxx-series are all based on the “squared” length design rather than the “rectangular” length design that the 7800GS has.

Google yields nothing either...but I suppose you could always go ghetto, and mod an old CPU cooler to it or something? Buy some ramsinks as well and it could work quite nicely.