Seriously, what sort of conclusions does this "article" even make? They say that it is somehow Window's fault that their software stops working because a DLL is replaced, because you know, somehow programs are supposed to run after you change parts of them. Next thing you know, they'll blame Windows for breaking their graphics card after they deleted their graphics driver.
As for programs modifying the firewall, that has been implemented since the Windows XP firewall at least. Run an iTunes install and you'll see all the exceptions that Apple puts into the firewall for their own software. Hell, perhaps we should blame Windows for letting the iTunes installer put Bonjour and Apple Updater and QuickTime on your computer as well? Clearly, they are allowing software vendors to put crapware on your machine!