Ultimately you should be able to use your C compiler and generate wasm files directly, rather than go through asm.js.

There is an experimental backend of LLVM that you can try, but it will require building LLVM from source currently. Emscripten has an option to do this automatically, I believe.

You can also write the AST format by hand, which IMO is much easier to do than writing asm.js by hand, just more verbose. I wouldn't advise anyone do this, as the format has been changing over time.

Finally, there is work on specifying a true "text format" that is meant to be used with view-source and directly maps to the binary format. You can see some proposals if you look at the pull requests in the design repo. When a proposal is accepted and we implement the tooling, you will be able to generate a binary directly from this format, which will be much nicer.