I've seen this movie a few times. Never really noticed it before, but this came out a few years after District 9 and that scene from Inglorious B******s about King King.
This is where it gets nasty
The film is set in the 70s with rise of crime right before the crack epidemic. The post war suburb is hollowed out as the economy tanks right before industrial jobs like the ones in the film go away. So the alien could also be a NAFTA commentary about Hispanics as well.
The most intimate deaths in the film are of black people. A lot of other ones are simply cutaways. The scientist and the second in command especially. The end of the movie is basically just accepting the past, letting go. Making the best of what you have now. No crying over spilled milk.