Ultimately the problem is that the game cannot assume you have done anything but the MSQ. Everything else is optional, so having side-story characters show up or be referenced further down the line is out of the question. It's just easier to kill them off or have them leave the narrative (as Alisae does) than have to come up with a way to have them come back after "their story" is already finished. The status quo must be preserved, which is probably why Nanamo ended up still alive after 2.5.5's climax. You could get a line or two, and usually only in other "side" content (e.g. Rammbroes mentioning NOAH during the SMN 50+ quest if you finished the World of Darkness), but that's about all I would expect.

Will Mide be killed off while waxing about how her ideal Alexander was perfect, and it's only because the Illuminai perverted it that things went wrong? Too early to say. Chances aren't really in her favor, though. The problem is that when an NPC is made for a specific sub-plot, and then that sub-plot is resolved, they don't really have anything to do... so they end up sitting around with their thumbs up their asses until the writers can come up with something for them to do. It's either that, have them go wander the world (Alisae), or "kill" them off (G'raha). Even MSQ NPCs are hard to figure out what to do with after their story arc is resolved; while killing them off is a bit predictable (and sadly blasé in XIV these days), it's better than having them sitting around doing nothing like WoW's racial leaders (most of whom do nothing during any given expansion).