The ghosts at the ruined alchemy shop will spoil the plot bigtime but they aren't actually related to the Xenka bug. (It was thought that the out-of-sequence plot reveal might be messing up the triggers, but investigation of the flags during Exult development showed that it didn't.) Regardless, the ghosts shouldn't actually be giving you that dialogue!
The problem is actually caused by the serpent staff pickup; the "egg" (code trigger object) is particular about how you pick up the staff, and if you do it incorrectly then the flag isn't set and Xenka will never talk about sacrifice because the game thinks you don't have the staff yet.
IIRC, the Exult team planned to fix this by having the code check whether the staff was in inventory rather than relying on the pickup flag, but I don't know whether they got around to it. If you aren't sure about the staff then just leave it be until you've completed every other step to trigger Xenka's dialogue option, then go back there, save the game, pick it up, and go talk to her. If it doesn't work, reload and try again. I know that being too far away is one cause of the flag not being set properly (get close to the staff before grabbing it), and some methods of putting it in your inventory don't work, although I don't remember which they are (dragging it over the in-game sprite, into backpack/bag, other party member, etc).