I'd have to see the source code and the translated code to form any judgement about that.
AFAIK Emscripten is not a source-to-source translator. It is a LLVM backend. asm2js code is very cryptic. You basically have everything in one big array and weird javascript expressions that are meant to ensure that expressions are taken as typed by the JIT. You cannot reasonably expect to be able to modify the output by hand.
