You might try WinMerge. I use the portable version from PortableApps.com
http://portableapps.com/apps/utiliti...merge_portable
I've never used it before with epub, but did a fast run-through for testing.
It won't recognize files with the epub file extension, but if you re-name the extension to .ZIP, WinMerge can compare each of the files in the two zips.
If all the (x)html files are named the same in both archives, WinMerge can compare them in a split-pane window, line by line.
If the (x)html files are named differently, WinMerge can open the two files you select to compare in two Notepad windows.
The Help file is quite straight-forward and easy to follow.
Like I said, a fast run-through, there might be glitches and gotchas that I didn't encounter.
Edited to Add: Yes, you would have to save an old version and a new version of the epub to compare. Is that a deal-breaker?