Prevent the github/fetch shim actually shimming, and assign it instead to a variable.

fetchAntiShim.js

// brfs is needed to use this anti-shim.
var fs = require('fs');
var functionBody = [
  'var window = {};',
  fs.readFileSync(__dirname + '/path/to/node_modules/fetch/fetch.js', 'utf8'), // Fix the path for your needs.
  'return window.fetch;'
].join('\n');

// Assigns a function fetch function to module.exports. Here I elect to use a native Promise implementation (or
// polyfilled). This is trivial to adapt into a library that can take a user defined Promise.
module.exports = new Function('Promise', functionBody)(Promise);

// Now require using this module. In the same directory: var fetch = require('./fetch');