After unzipping the patch into the P2 folder, try running darkfix.exe instead of using the GOG icon (the patch installs side-by-side with the GOG installation and doesn't override the DOS EXE). This patch is based on the Win95 exe, so it should work better.
It's odd though, the DOS EXE released by GOG was apparently patched with an official Origin fix released back in 1997, which should have fixed the bug at least in theory.
You shouldn't need to start the game from scratch, if you have a savegame before paying Hal Taffin, going back to that point and choosing not to pay him should work i think.
In any case, I'd like to study this bug more in detail. Could you post your savegames so I could poke around a bit?