import html from './example.html';

$ npm install --save-dev babel-plugin-ignore-html-and-css-imports

.babelrc

{
  "plugins": ["ignore-html-and-css-imports"]
}

$ babel --plugins ignore-html-and-css-imports script.js

require("babel-core").transform("code", {
  plugins: ["transform-ignore-html-and-css-imports"]
});

You can configure what extensions to remove by adding an optional removeExtensions option.

{
  "plugins": [
    [
      "ignore-html-and-css-imports",
      {
        "removeExtensions": [".png"]
      }
    ]
  ]
}

Initially based on yeiniel/babel-plugin-transform-html-import-to-string which turned out still not to work properly in Meteor - and since we didn't need the string at all, we've decided to change it a bit.