well, if this is in a cabinet that has joysticks and buttons as well as guns, it would be easy to do. just tap into your existing ipac or other encoder for the reload pedal. you could mount a jack of somekind at the bottom of the cabinet so you could easily detach the pedal when you dont want to use it. or perhaps have the pedal mounted on a flip down panel at the bottom of the cabinet, that folds up into the cabinet when not needed.
for anyone using guncon2 guns on a ps2, you just plug in a controller to the gamepad port and you can use any of the buttons as reload. you can then hack the controller so that you can attach a pedal to one of the buttons. the same applies to the PC, you just wire a switch to your regular encoder.
even on a cabinet that is just for gun games, you would still need some kind of encoder to handle the start and coin buttons, as well as some kind of system to select which game you want to play...so it should not be too hard...there would be no need to tap into the gun