Oooh, nice variation. Have to admit, I haven't worked out an "Aerith lives" AU yet, but there's at least one AU I'm working on where the long-term plot arc might well fit the bill... or at least it's alongside the original canon with "Aerith isn't anywhere near as dead as she's thought to be".

But I like speculating about this one - I suspect it was Jenova who was most terrified by the realisation that Chaos (who was, after all, designed by the Ancients/Lifestream to be a sort of filtering and purifying device for the Lifestream prior to Omega's departure) was loose and able to come after her - and she'd definitely be identifiable as a major contaminant of the Lifestream should Omega be rising. Plus, of course, Omega rising essentially means she's welcome to what's left of the Planet after Omega has gone, but I sincerely doubt bare rock is of any use to her, given she's largely organic herself.