We're reusing the stuff we built for the Try iOS course we came out with late last year. I've looked into Emscripten for this and from what I saw it really wouldn't work with this course, although maybe I missed something?
You could always boot the VM with an image that contains the compiler and run there. If it truly does boot faster than the results take otherwise then you could move it all into javascript that way, and not have to worry as much about the infrastructure around it.
Fabrice Bellard's browser-based Linux boots in less time than this prints out "Hello, world!"