Originally you could disable the intro movies and logos with the -nologos command line argument, but that doesn't work with the GOG loader.
There is a workaround to disable the logos. You can simply rename the files or move them to another folder to prevent them loading.
in psg\resource\videos move or rename:
infogrames.smk
IWar.smk
logo.smk
end.smk
Now (apart from the intro movie) the game will start up and shut down much quicker.

Actually it doesn't seem like you have to use the GOG loader for the game to work, and can simply use the original exe along with any command line argument such as -nologos.
I'm running the game now with iwar.exe -b -16 -800x600 -nologos and it works flawlessly, no shift-q bug or anything. Before the GOG release, with an install from the original CDs, I started the game in exactly the same way but did get the shift-q bug.
Whatever GOG did to fix things, it doesn't seem to be in the loader.
Still, good to know for whoever runs the game with the loader.

Ah, thanks for that. I thought it was the loader that possibly fixed the game.