This should only be an option. If you want to compare two files the size of the files should be checked and you should get a warning if they are very big. If they are small enough a bitwise comparison should be possible.
This could be an example (quite bad because its in german and I'm not a designer ... if someone could make a better one it would be nice):
http://www.martin-thoma.de/ubuntu/warning.png
Kompare allows you to compare and merge text-files (and I think there are Gnome equivalents like gtkdiff and meld). So we could just link this button to one of these apps.