Considering every story update comes with a major patch, I think that SE could easily replace NPCs when they show up in a small amount of sidequests like Nanamo has. It would just be part of the update.

That or they could just leave the quests the way that they are, and still kill the character. Narrative inconsistencies are all ready in the game, anyway. Things like the dhomans showing up late in the story, but you can still do the ninja quests while in the 2.0 story, where they reference just having arrived in eorzea. Or Rev Toll's development having no visible significance to anyone jumping into the game right now.