There are already places in game that have a different appearance and different NPCs depending on how you've progressed in the game. One easy example is the setting for the Moogle beast tribe quests - that area gets refurbished and built up over the course of the quests. All that really needs to be done is ensure that in "rebuilding" Ishgard, any place that is an obstacle to movement now needs to remain and obstacle after it's rebuilt, so that newer players don't see older players walking around on thin air or whatever. (Giant hole in the ground? After being rebuilt, put a potted plant there so people still can't walk there. That kind of thing.) Stuff like the crawling wounded soldiers are even easier to be rid of.
It basically boils down to how much SE is willing to invest in this kind of thing, and I'm guessing that this kind of thing would be pretty low on their list of priorities.
Housing in Dun Scaith, though, is another matter entirely. Dun Scaith is an instanced area. If they were to make Dun Scaith housing, it would be a separate instance from the raid instance. There'd be no danger of folks running Dun Scaith and passing by a ginormous Piassa-themed mansion with six Christmas trees in the front yard, because the Dun Scaith housing area is a completely different zone from the Dun Scaith raid area. It just is designed to look like Dun Scaith. Consider Haukke Manor. Just because Haukke Manor was involved in last year's Halloween event did not prevent players from continuing to run Haukke Manor for their Main Scenario progression. Folks didn't enter Haukke Manor (Hard) to find it filled with wacky decorations, either - the Halloween instance was a completely separate thing from the Haukke Manor and Haukke Manor (Hard) instances.
I don't actually think that Dun Scaith will become a housing area, but the fact that a raid takes place there is not an obstacle.
