ICV2's Steve Bennett has this interesting take on the series:
"Of course we’re supposed to want our heroes to kill them; they are, finally, what I've been asking for all along, a fantasy stand-in for Al-Qaeda, religious fanatics bent on destroying everything that makes us who were are because being them is so much better. At last there are make-believe terrorists our heroes can punch in the face (and then some) without it seeming inappropriate or in bad taste. So I’m guessing the audience these comics are intended for is cooing “cool!” every time they see a Skrull reduced to a fine green mist."
If this was Marvel's intent, brilliant! They certainly had their finger on the pulse of current events vis a vis the political divide the country has/had been facing in last year's big event series, "Civil War," in which heroes fought themselves over a ideological clash sparked from a major disaster which left many Americans dead . The phrase "you're either with us or against us" was probably one the most often used in American superhero comics from 2001-2008.
I don't think it's beyond the realm of possibility that the series is supposed to offer us a little bit of sublimated revenge. And guilt free too, since the Skrulls are attacking the world, not just the U.S. , and they are highly othered, not even our species. But the macro-level politics might be evidence to the contrary of Bennett's point as well. The tag line of "Secret Invasion" is "Who Can You Trust?" which to me seems to get more to the internal American body politic and culture than to our global affairs, but I have always been inclined to paranoia to begin with, so maybe the connections I'm growing are even more local than I'd like to admit.
Go read Bennett's complete thoughts here. The Skrull stuff is about halfway down, and there's some naked Batmen characters for your viewing entertainment (a la Austin Powers) in there as well.