I think it is obvious that Alan Moore, with his backstory of the creation of the alien monster, has insinuated the intellectual class' unintentionally malvolent role in practically every massive social movements that ended in bad taste, including but not limited to communism, socialism and nazism, whose more pressing example is stated clearly in Paul Rahe's essay The Intellectual as Courtier
Somehow it is also an evidence of his effort of trying to stuff too much underlying context into his plot, which is even beyond his ability to control, and making its ending unpleasantly awkward thus unfit to the cinematic version. I believe the alteration is required, because facing a broader audience you have to make the overall story less plausible and imagining an alien octopus is something corny in our early 21st century Sci-fi.
However the message is still there, despite significantly weakened. The attacks are now focusing only on those scientists helped buiding the doomsday machine. But even that change reflects the tide of our society: the scientists, replacing clergies and legislators, are now the most appealing and reliable individuals to the public, yet their cooperation with authority is tightened like never before. I feel a bit dissapointed that this message has sliped so many's eyes.