ComponentSoftware's
free CSDiff file comparison tool will also compare epubs, if you change the file extension to .zip.
You'll need to run CSDiff once and change the Analyze option to Folder. You'll also need to enable the two check boxes. (Once you're done, click OK and close the app.)
After you've changed these options, all you have to do is select two renamed epubs and drag & drop them on the CSDiff shortcut.