Your approach was nearly correct. I am using the following code to open the response text in a new window (not specific to Werkzeug or Flask at all):

var w = window.open('', 'debug_stuff', 'width=540,height=150');
w.document.open();
w.document.write(response.responseText);
w.document.close();

The last line is the most important. Without it, the code would behave as yours -- it would not execute any JavaScript, because the browser doesn't know the DOM has been fully loaded.