No, it would work. You just flip the HSI chip around. That is how they make AGP cards with new GPUs like the 7600GS (http://www.newegg.com/Product/Product.asp?Item=N82E16814127219) See the angled heatsink below the circular one? That is on the HSI chip that converts PCIe to AGP and vice versaThere is one for AGP to fit in a PCI-E slot (8x can go to 16x)
It would be impossible to go from PCI-E to AGP (8 lanes of the 16X would have nowhere to go)