RotMG is a cloud game
The game uses both Amazon EC2 and Google App Engine.
There'd be three approaches.
Offline play. Run everything on your own Linux servers.
Private cloud run by you. Buy the code from Rob and Alex, buy cloud space on Amazon and Google, and run the code there.
Private cloud run by them. Pay Rob and Alex to run a private server for you.
The EC2 servers could conceivably be run offline, if (a) Rob and Alex wanted to release the code (they don't), and if (b) people are willing to buy custom Linux servers that can run the code (it doesn't run on Windows, and you'd need several high end Linux machines to set up the game).
The App Engine servers would be harder to run offline. They tap into Google's proprietary database system, distributed file system, web scalability architecture, and other Google services, none of which are available to run on your own machines. They also run on Google's custom Linux servers (custom kernels, custom libraries, etc.) and not on a regular Linux machine. These custom servers aren't something you can buy. Instead, you'd have to write new code to match the APIs they offer and simulate what their cloud does, or you might be able to buy this from a third party.
The SWF is just the graphical part that runs on your browser; most of the game is written in C++ and runs in the cloud. I'm guessing RotMG's cloud is actually spread out over many thousands of machines.
The game is not designed to run on your own non-cloud servers. However, it'd be possible to make it work with a private cloud on Amazon and Google servers, either with you buying the server code from them, or with them running them for a fee. It'd take a lot of work on Rob and Alex's part, and I think they're unlikely to work on this, unless a lot of people would be willing to pay for this. It'd take away from the other things they want to do. (What would you pay to run a cloud?) They can afford the shared cloud only because there are lots of players.
It may be possible for someone to write their own game servers from scratch, in a way that is compatible with the SWF. I'd be impressed if you did this. Really impressed.