They really should add an option to get unsupported files that lets people download things that have been stripped out.
I'd go as far to request ISO and disk images for games that have been released in programs like DosBox or ScummVM. Most people won't use them, but for those that want to do the work themselves should have a chance. Just make sure to put up "Nothing on this download is supported in any way!" and make the person click OK to get it.
Or they can just stop stripping them out in the first place, really what is the point in taking them out? Honestly the average user here are not going to go poking around and play with those files since they just use the shortcuts GOG gives them and call it the day. The average peson I find that goes poking around the directories and uses those files are those who know what there doing or want to try them out and see if they can get it running and those people are not going to be hammering suppourt with complaints about it if they don't work at worst that they will do is maybe post in the game's forums much like some linux users do
This has been brought up many times before and the answer has always been, it's all about the quality of GOG's releases. Even if they were to release the full content, ISOs, etc. with a warning that that stuff is not supported, people are going to look for support for it and it gives the (erroneous) impression that GOG is selling a broken product. For a small company like GOG, that is severely damaging to the brand, more damaging than it would be to simply not offer or remove the non-functional stuff. In this particular case, it does sound like the removal had less to do with protecting the brand and more to do with expediting the release, but for nearly all the others, that is not the case.