It sounds difficult to remap the keys since the input comes from a different line (POTGO vs keyboard). You would need an emulator for this
However I'm not sure it's not possible to simulate a keypress from a joystick input by writing in CIA regs??? I'm no CIA expert.
Whdload uses VBR relocation and could check joypad state at each VBLANK without problems like it does for QUITKEY.
ATM the only way is that the slave does the job. But it's specific to each game, even if some solution could be found for kickemu games (those games have greater chance to run on a CD32 WITHOUT whdload though