I think that she disappears after a split-second if you return to the church before her death. If you go back later, though, her ghost doesn't vanish until you try to walk up to her. That's why I think that the earlier appearance is a glitch, and the later one is deliberate.

I remember the first time I saw her there... back in '99 or so, I guess. I was all like

"omg omg omg!"

*runs toward her*

*Aeris disappears*

;__________;