[Edited to include pertinent comments]

One should be able to precompile files and pass them to systemjs-hmr for a quicker reload cycle.

Something like this

System.reload("app/a.js", {
   from: {
      "app/a.js": {
         source: 'module a source code'
      },
      "app/b.js": {
         source: 'module b source code'
      },
   }
})

So that the hot-loader can precompile and send over the changed files. This will essentially only save the load time latencies that would be incurred by System.import