I think, it is posible to make a litle bit more dificult to read (for real - to read correctly) contens of external EEPROM. You can make unnormal HW. For example use PLD and change internaly data lines, Adres lines and so on. In this case, as an example replace data bit 5 with 2. there is no difference for uC (of corse, you have to do this in your bin file too!) but it will be dificult for thief. And you can do what you want with Adresses as well ;)

That is not secure for 100% of course, but it will make nervous the man, who will try to solve this ;)