If they ask for a security clearance or are willing to sponsor it, it probably has to do with that $600M private AWS instance for the CIA.
But yes if you have a clearance here you can pretty much walk out of the building if you don't like your job and walk into the next one and they'll give you one. (That's the joke anyway).
Edit: I found a map with the C2S region on it, and it does appear to be in the VA/MD area.
No, anything remotely close to the US government requires a full citizenship. I got slammed by that when I was in the middle of applications for scientific software companies which did government contracting on the side.
Some excellent naming there ;)
Also worked for the military and we had a variety of citizens, non-citizens, green card holders and non-green card holders. We had to go through silly gymnastics on who can talk about what and work on what depending on their status.
I've personally known permanent residents to work in government contracting.
For your case, if I had to guess, it's probably the physical building/facility they required you to work at had restrictions on unescorted non-citizens.
http://docs.aws.amazon.com/govcloud-us/latest/UserGuide/gett...
"§ 120.15 U.S. person. U.S. person means a person (as defined in §120.14 of this part) who is a lawful permanent resident as defined by 8 U.S.C. 1101(a)(20) or who is a protected individual as defined by 8 U.S.C. 1324b(a)(3). It also means any corporation, business association, partnership, society, trust, or any other entity, organization or group that is incorporated to do business in the United States. It also includes any governmental (federal, state or local) entity. It does not include any foreign person as defined in §120.16 of this part. "
http://pmddtc.state.gov/regulations_laws/documents/official_...
Though I'm sure AWS does lots of work with US government agencies in us-east-1, so it's not surprising that a government clearance might be required for some of it.
As for us-east-1, it all began in Chantilly in an existing low-rise building you could mistake for rentable office space, then expanded to several different sites between Sterling, Ashburn, and the airport itself, and perhaps surprisingly, to another place where famous battles were fought. Finally, they have a site a bit further away, near where Disney was going to build a theme park. That's where they want to expand more, but first they have to convince the power company to get them a dedicated line, instead of being fed from the same place as the battlefield.
Some sources:
https://aws.amazon.com/blogs/aws/new-aws-govcloud-us-region/
http://www.oregonlive.com/silicon-forest/index.ssf/2011/11/a...
http://www.oregonlive.com/silicon-forest/index.ssf/2011/10/a...
Some people operate directly with the intelligence agencies (and work on their campuses as part of their duties for AWS). These people often handle sensitive data and therefore need clearance. Amazon often hires individuals who are located near intelligence services to ease this.
There is plenty of governmental work out there that mandates certain levels of clearance. Even big consulting firms like Booz Allen or Accenture will require it for certain hires.