If they remake FF7 and do anything different regarding Aeris, the only thing I could see them doing is adding a cutscene in the church, something like after the death of aeris, in disc 2 when you can return to the church. The first time you go to enter the church, Cloud will ask the others to wait outside. He goes in and Aeris is there (spirit) and they have a conversation about his guilt and feelings about it all, similar to the scenes in Advent Children

Imo thats my personal theory to the ghost in the church glitch, that a scene like that may have initially been planned, but later scrapped due to time restraints.