Right, before I lose my patience and rip someone's spleen out for asking: there is no way to get a working Aeris character for disc 2+3, short of rescripting that entire half of the game. Which we can't do, not even technically (yet). And speaking as a programmer, there is no evidence to support there were ever plans for anything else than for her to die. Yes she does have some lines at a few select places through-out the rest of the game, but there is also an overwhelming majority of non-existant lines. The few that are there could be simply because they hadn't fully decided to which places you should be able to go before Aeris dies, and so she has some lines in places she, in the end, was never able to visit. Isolated incidents like "ghost in the church" and similar stuff with no deeper support in the story should never be seen as having a deeper meaning, in fact I bet the game scripter that wrote that ghost Aeris easter egg into the game on his spare time is having a good time watching the world-wide speculation frenzy that caused.
Technically speaking, it's not so much a problem of Aeris not having any lines, it's more a case of Aeris not existing in those places. In each and every FF7 location, all the characters are scripted into the scene (as the on-screen characters you see), and then the ones that are actually supposed to appear on screen are selected from those based on your current party. Each scripted character can have different lines and actions, thus the actual dialog you get can depend on the current party. If Aeris is in your party, but she does not have a scripted on-screen representation for her to "step into", the game engine will freak out (a little bit like dereferencing a null pointer, though the game script engine is of course a bit more abstracted than that).