Sort of. This can obviously be non-blocking and redirected to whatever stdin-ish receiver you prefer:

  alert('whatever');

This cannot:

  const answer = confirm('A querstion?');
  const value = doSomethingWithUserInput(answer);
  return doSomethingWithValue(value);

The API depends on it blocking the main thread, and removing that expectation is effectively just as disruptive as removing the feature entirely: non-abusive usage would have no reason to call this function if not to block for user input. Introducing some magical suspension of the stack like async/await or generators would break assumptions about the entire concurrent execution model of the language (the inverse problem of “colored functions”, infectious async/await etc).

The best thing they can do without removing the API is provide an escape hatch, which most browsers already do when alert &co are called multiple times in quick succession.