I'm not sure if Linux is setup to handle InnoSetup files natively. (At least yet.)
If those files do use nsis in some way, I'm not sure how well they can be extracted.
I tried 7z (version 4.58 ) but it said that it was an unsupported archive.
I tried an uninstaller called peazip which is supposedly able to handle nsis files, but it seemed to have some problems with the files, however I have never used that extractor before today, so I can say little about it. (Perhaps someone else might be able to do a better job.)
Theoretically I wouldn't be surprised if there might be some tool, somewhere, that might be able to do the job, but frankly I think it would be much simpler to just install the games under dosbox, since that would be where I need to run them anyways.
I never even bothered trying to run the files under wine, as personally I would prefer to use dosbox, and for wine, I have in the past played GK2 under wine without needing the installer. (How much that has changed through the various wine versions, I cannot say, which is a large part of the reason I would prefer to use dosbox for apps whenever possible.)

Like Endroz's installer mine also concatenates the resources from all 6 CDs to install completely to the HDD, so the installer is not just to set it up in DOSBox. I only suggested WINE for the installer, not to run the game itself. The main thing would be to get Endroz's UniSCI to work under other platforms. Unpacking the installer would not do much good, as relevant included files are available elsewhere and does not accomplish the main task of joining the 6 CDs. Anyway, as I said, I'm using NSIS, not InnoSetup and 7-Zip extract files from an NSIS installer, even if it can't decompile the script.

I am also wondering a little more about Mac, as Linux users would probably be more likely or more willing to work it out manually on their own. In the end, the only reasonable solution might be to just have separate scripts for Windows, Mac and Linux.

I'm not sure if this is what you might be interested in, but there is a place set up to handle scripts for running/installing apps for Linux.
http://www.playonlinux.com/en
This specific site requires that Playonlinux be installed, and tends to focus on running windows apps under wine, but there are several dos games there.
Alternatively there is another place that has created installers for linux games.
http://liflg.org/ (loki installers for linux games)
using the loki setup tools http://icculus.org/loki_setup/
At one point liflg used to make installers to install windows games which would then run under wine, but they stopped for various reasons. Perhaps it might be possible to use the loki tools as an installer.
I'm afraid I don't know how useful this is to you.