Theoretically, if you had the time (and patience) you could add Aeris back in all fields where there is an event involving the whole party, and where Aeris is not scripted in cos she's, well, dead. In addition if you did the lot you'd have to create some sort of Aeris resurrection scene since it'd be a bit odd for her to die, drop her in the lake in the City of the Ancients, only for her to turn up in your party when you leave.
Frankly, it's quite a lot of fields, and you would need to create a patch for a lot of files since you can't go round distributing the fields you've edited since it's akin to sharing the flevel.lgp as a whole (i.e, legally dodgy). The question is really whether it's worth it, and if anyone has the patience to do it.