The Via880 Chipset was always a bit on the slow side and its limited FSB tops out at Kentsfield. The nforce3-combo is officially capable of Deneb. Inofficially, I would expect limited Yorkfield operation (board probably overclocked to its limit to get a core 9000 to stock-clock) and unrestricted Thuban operation, respectively. Of course most applications of interest do V5 operation would be singlecore, so the Intel plattform might perform better in real life, but you can get more raw power with AMD.
Regarding converters:
I'm pretty sure, that there was no other AGP-PCIe-converter for sale, then the ATOP. And being stuck with a So478 P4EE, I kept three eyes open for any to appear.
However, somewhere deep, deep down in pre-PCIe-times I seem to remember AGP-PCI-X-converters for professionell use. Though I can't remember, wether they were from or to PCI-X and with half the world to stupid to distinguish -X and -E, it seems impossible to google for such old off-mainstream hardware. However, if one could find such an converter...
It wouldn't look any cleaner, but it would give full AGP-speed.
BTW @trevor: Is your setup operating at PCI33 oder PCI66? (and have you tried getting higher? After all, the 6000 was always limited by the onboard-bus, so the bridge might tollerate interface overclocking, as long as the amount of data per clock stays low due to the PCI-bottleneck)