korell: I would imagine that the GOG Galaxy folder structure is inert if you don't actually have Galaxy installed, so you can probably just delete them.
IronArcturus: When I delete the Galaxy folders they are immediately recreated once the game is restarted. It has to be a bug since other GOG games may use Galaxy but they don't create the folders.
In that case, it's going to be one that needs to be raised with GOG Support directly, as it will be down to how they've packaged the game to work. It may be that there is a reason behind it, such as making it easy for the game to be imported into GOG Galaxy should the user decide to make use of it for multiplayer after having initially used the Classic Installer, though I thought that Doom 3 (the other game you've seen with this issue) didn't have multiplayer other than forced via LAN. Or it may be an oversight in GOG packaging the different GOG Galaxy and Classic installers.