There's talk of using RandyT's LED-Wiz or Bubbading's board to control devices other than LEDs. Maybe you could use one to control a circuit that swaps the controls. You'd need MAME to trigger the device when the players change turns... SirPoonga and Gl.tter have both done work on getting MAME to trigger events, maybe you could put something together.
Or, it might be easier to just wire a switch that lets you make the ground loop for only 1 set of controls be active at the same time. Your players would have to switch it by hand, but it's certainly easier to build.
Out of curiosity, why? Building a dual-monitor machine, or two separate-but-linked machines?