the Atari ST version is already cracked.. so you could just port the crack as well.
I wonder about the probability of using something like IRA to disassenble the code, then go through it and document the Atari ST hardware registers and ROM calls (so it's easier to know when trying to re-code it for Amiga), then trying to recompile it afterwards. After all, if you do a straight 68000 re-assembly, but change all the hardware registers/ROM calls etc. to what the Amiga hardware uses - surely the code should work? It won't be as fast as an optimised Amiga version using the Blitter etc. but it should still work (in theory). Hence attempting some relatively simple game (like an RPG) would have to be better as a first attempt, as you shouldn't be worrying too much about timing, interrupts etc. as you would be with an arcade game.
At the very worst I'm guessing you could use an IBM and an Atari ST emulator with breakpoints/disassembler et. built in to aide in the cross-compiling.
I'm not saying it'd be a quick process, but it sure should be a heck of a lot easier propostion now with emulators and virtual machines etc.etc.
I'm sure I found somewhere on the 'net where someone had disassembled the original BBC 6502 'ELITE' and had cross compiled it to another CPU. I'll go looking..
EDIT: not quite what I was looking for, but it's a start - disassembled a BBC game named 'Dare Devil Dennis' to 'C', then recompiled to run under the Archimedes OS.