Not sure if you’re still looking for an answer to this, but now you can include the beta version of uglifyjs-webpack-plugin as a webpack plugin and it’ll use uglify-es which can minify ES6 code.
npm install uglifyjs-webpack-plugin
and then in your webpack.config.js:
const Uglify = require("uglifyjs-webpack-plugin");
module.exports = {
entry: ...,
output: ...,
plugins: [
new Uglify()
]
};