I realise you say the ghost can appear with Aeris around, but then she has lines of dialogue which she speaks as part of the team after
(SPOILER)she gulps it down.
I guess I'm willing to believe it was another mistake. There's some interesting information on FF7 Citadel about what may have truly been intended for Aeris, such as... well, I'll wrap it in spoiler tags in case you wanna read it all yourself.
(SPOILER)Thanks to software used to decompile the game's files, evidence seems to suggest that Aeris' abrupt dismissal from the land of the living was not supposed to occur until the middle of disc 2 after the event in which Cloud gives the Black Materia to Sephiroth for the second time. Obviously, were this even the case, this idea was cancelled pretty early on.