I was assuming you mean "The end of disc 2" when talking about "that part of the game" since that's the part of the game that deals with Eiko's story.
But there's lots of stuff in Madain Sari and the Iifa Tree that have thankfully little to do with Eiko and her insistence on marrying Zidane.
--
http://img710.imageshack.us/img710/8516/whatisdesiresig.gif