Instead it’s preferable to pass webpack ES2015 code (which enables the new tree shaking feature) and then transform the entire bundle (or each chunk) into ES5 in one operation. That’s the purpose of babel-webpack-plugin:babel-webpack-plugin.
It works in almost exactly the same way as UglifyJsPlugin. Just add to the plugins list (before UglifyJs if you’re using it) and the code will be transformed from ES2015 to ES5 all in one go.
See the README on github for options