current-system is just another immutable package that symlinks stuff in environment.systemPackages (built with buildEnv).
You could inject extra code to environment.extraSetup NixOS option to remove the desktop files from the symlink tree. But that might require manual reification of symlinks if you are unlucky and the files you want to remove are inside a symlink to a directory in another package. And it will not help you if a package looks directly to g-c-c Nix store path, you would need to update the references in the package. At that point, you might want to use system.replaceRuntimeDependencies hack but that is a bit tricky.
Alternately, you could install a package with higher priority to environment.systemPackages, that would contain a dummy version of the files you want to remove. But again, that will not work if a package looks directly to g-c-c Nix store path.
Anyway, this is getting off-topic so please open a new thread if you want discuss this avenue further.