I believe the Cypress board requires a Programming Tool that discovers the device and downloads a new custom firmware. It requires a Service called CyMiniProg3Service to be running that recognizes the device when plugged in and reconfigures it. It requires a DLL called NICYAPI.dll which does the lower level USB communications.
If you can get those three items ported over, or equivalent substitutions, you are correct, it will be simple.
http://www.cypress.com/?app=forum&id=2492&rID=72383
This forum thread may be related to the first item. I didn't search the second. The third item, along with the custom firmware were made by an NI employee -- in volunteer mode.
My point is, it doesn't hurt to ask "why" or "what would it take" questions. Those typically lead to good investigations and research and learning. But assuming something is simple can make trivialize the other people's work.
I can assure you that nobody has an agenda to keep linux or other operating systems out of the FRC system. In fact, the blue 2009 DS ran linux.
Greg McKaskle