when Scott's cross-compiled Quake to SWF he used SDL as the graphics layer. I looked at the Quake project a few months ago but couldn't compile it with the rest. I ended up using http://github.com/mkr3142/QuakeFlash, which does not use SDL.
I vaguely remember that compiling SDL was not the problem.
Have you tried downloading the SDL source and compiling it with Alchemy?
That might just work.