In fairness, the babel approach to module handling is probably better than an in-browser es6 module implementation, or what may follow... compatibility with npm packages (cjs) will be significant for a while.
My understanding is that V8 will provide hooks that parse the module imports, then delegate to the embedder to fetch the actual source code and hand it back to V8 to load. I'd expect that the Node implementation of these hooks would work the same way as the existing require() machinery, so that existing libraries will continue to work.