I've seen some GOG games before that left old, defunct protection files in the installation from games that were originally protected by safedisc, etc. Not a big deal, but with Beyond Divinity, it's getting a bit carried away:
div.wpj and div.alf (WDasm disassmbly of div.exe. Text file. 92MB!)
protect.dll (old starforce protection library. No longer needed)
resource.dat (old starforce file system SFFS container. No longer needed)
This all amounts to over 100MB of useless files that waste disk space and cost GOG bandwidth.

That would be a valid complaint. You should contact GOG support about the issue. There may be a legitimate reason for leaving the files intact but only GOG could answer that question. I would prefer a smaller package as well.