Large companies work by inertia. Google is actually more agile for its size, but it's still a big company and ruled by inertia.
In a large company, the majority of people don't know each other, and don't communicate on a daily basis. This means that things of interest get passed from person to person, usually by email, and so the original intent of the message tends to get lost due to the 3rd or 4th reader having no idea what kind of person the original writer is, what his writing style is, whether he's being serious or joking, etc.
As a result, you end up with lots of requests for clarification, especially where it's an event that falls outside of the normal routine. It takes a lot to rile up a company, but Andrew did it expertly, pushing all the buttons his background in sociology and politics gave him a solid understanding of.
Notice how it went through three separate "request for clarification" requests, each more formal than the last. Each time, he responded in a passive-aggressive manner that re-pushed those same buttons.
As it pushed its way through the various departments and echelons of the company, such a message would become more and more threatening as the person became less and less known. People go into CYA mode (better safe than sorry), the company momentum changes and things start rolling.
Let's look at the course of events again:
1: Andrew is intercepted by someone who is probably a manager (notice his description "Agitated Chubby White Male", with the connotations of bourgeoisie).
2: The manager takes Andrew to explain the situation to security (pointing out that the security guard is a black man in a menial job, with "sedate" added for connotations of passively accepting his proletariat fate).
3: Security contacts Transvideo to get clarification from Andrew and find out his intentions (notice his description "so that the issue can be filtered and separated neatly into their bracketed accounts", with the connotations of the soulless bureocratic corporate machine).
At this point, the security department is unsure of Andrew's intentions. Was it just harmless curiosity? Is he a plant, trying to dig up dirt to embarrass Google? They can't know for sure, so they ask him to clarify his position.
What Andrew sends back is a passive-aggressive letter covering class, race, and labor, all hot button topics. His manager asks for even more clarification. People are getting very nervous at this point.
Andrew's response is political dynamite, once again using passive-aggressive techniques to all but accuse Google of racist discriminatory labor practices.
That someone with "backgrounds in sociology and political philosophy" wouldn't understand what panic his second letter would produce is incredibly hard to believe. In fact, Andrew's entire description is so slanted and colored that I'm inclined to suspect that he deliberately set about getting himself fired so that he could trumpet "Google is Evil!" from his blog, Michael Moore style.