Isn't this whole Campaign world a little (or a lot) racist?  The MiBs are basically Nazis, right?

The simple answer to this question is no.

My MiB campaign world is not Star Trek.  The aliens are not touchy-feely Vulcans or money-grubbing (but oh-so-cute!) Ferengi.  The Galaxy is a very dangerous place, and Earth is alienated by its lack of military and obvious political power.  It is only when a curious alien digs deep enough in various public records and makes some correct assumptions about certain people that human power becomes much more obvious than it is to the public eye.

Aliens don't like humans.  Some do, but they are either less powerful or insiginificant to matter to most of the big 200 most-powerful races.  I don't take the "I love you/you love me" take on the Universe.  Hell, if Americans were so quick to mistrust Communists because of their ideology then what are we likely to think of a race of creatures with fangs and claws?  What are they likely to think of us?

The PCs are not out to kill as many aliens as possible.  See the Adventures section for evidence of that.  The Golden Rule simply allows MiBs total leeway in completing their missions, as long as humans are not harmed in the process.  If I wanted to make the PCs Nazis, then I would have them slaughtering innocent aliens by the millions simply because these extraterrestrials happen to be the scapegoats of the month.  The Secret Masters see every single alien planet as a possible enemy, and take such steps as are necessary to prevent them from becoming a dangerous entity.

War has followed mankind since he rose from the ashes of the Cromagnons, and I doubt that a few centuries and a few laser pistols are going to change that.