The solutions:
1) Marvel make a northbridge with an AGP controller instead of a PCI-X controller → simple, everyone is happy
2) Genesi pay money for someone to make a PCI-X to AGP bridge chip. Costly, inefficient, higher latency, and possibly issues with full AGP compatibility. May require "August" chip to work correctly in the end.

I think the former is more likely, honestly. Then again, bbrv admitted in that thread on ANN that the Pegasos basically drives the AGP slot as a simple PCI device, without using any of the extra features of AGP. So who knows?