Just my $0.02:

Like most art, the viewer can draw his own conclusions. But frankly, I think the OP is onto something. Just as Invasion of the Body Snatchers used science fiction to address the "red scare" of the 1950's, Or how the giant bugs were a societal saftey valve to the idea that maybe radiation was going to cause some small problems to become gigantic, I think Kneale was, either conciously or unconciously, working the elements of the nazi horror into his storyline. Let's face it, the nazis and their ilk make GREAT villians!

The fact that they discover the "secret camp" where people are being put to work...
The people of the town not wanting to know what goes on there, so long as the work is good...
The townspeople becoming "marked" and then hauled away by a group of annonymous gun toting thugs...
The images of people who have been "taken over" by the alien thught process, working like zombies...
The minister escaping from the alien "gas chamber"...
The whole "trapped in a building" and surrounded by dark, military forces... very similar to a jewish ghetto.

And so on...

But I'm sure that Kneale, as a writer, probably had nothing but telling a good yard in mind... The "final solution" imagery just kind of bled into the thing simply because it was one of the most terrifying historical incidents he'd lived through. (Just as 9-11 has bled into movies like Cloverfeild.)