Yeah, using a jag pad in place of the joystick with access to only one button wouldn't be hard at all, but then again using Sega master system gamepads would be acceptable in this case, and they're probably easier to get than Jag Pads.
I still find it odd that the Amiga wired their ports up so that games could support more than one button, but Atari who more or less started it all (at least with the DB9 controllers) never improved upon it.
I had read that it accesses the hardware directly, that is why I was thinking a hardwired way to do it. And yes, a micro controller was what I was thinking (so you could assign say a space bar to button b, button A would be joystick, etc.) Granted it would have to be a programmable micro controller that would be similar to the connector for the CosmosEX, that allows USB keyboards.
Atari 8Bits: 800xl, 600xl, XEGS, 800, 130xe, 130xe (fully upgraded (soon!))
Atari STs: 1040STf (broken shifter), 1040STe, Mega STe, TT030, Falcon (CT60e, SuperVidel)