You could always program your own keyboard controller firmware.
Or just do what the Microsoft prototyping guys do and program a virtual COM port through USB interface, compatibility with the "legacy" limits of IBM's 8042 chip and scan code sets be damned. Mind you, this approach would only operate after your OS drivers are loaded up, so you'd still need a standard keyboard for POST and BIOS stuff. And oh yeah, it'd eat up a little bandwidth from one of your USB hubs.