My strategy is typically store MoonScript in separate files, then have build process that generates Lua and bundles that inside of whatever else. I wouldn't typically put it in a C file, but I might have the build system generate a hex encoded string as a header file. (This is actually how I build the MoonScript source into a single exe for Windows builds)

I recommend doing the MoonScript compile time at program build time to avoid any unnecessary compilation during runtime.