[q=Phoenix 17]In what way did Cloud and Co. fix most of the problem?
[/q]
They killed Jenova, killed Sephiroth (three times) and released Holy from its confinement in doing so. That probably counts as fixing most of the problem.
If Holy was going to kill ALL Humans, it would've started with Cloud and Co, yet as I've said they were closer to Holy than anyone else and weren't affected in the least. Holy would not annihilate an entire species just because a few of them weren't terribly nice. That kind of rampant destruction would make it little better than Meteor. Bugenhagen said that "all that is bad will disappear..." The humans in FFVII aren't funadamentally 'bad' or 'evil'. Even some of Shinra's top executives were merely misguided and naive, rather than 'evil'. It's their creations - such as Mako reactors - which were causing true harm to the Planet.
Anyway, here's something to think about... Red XIII killed a lot of people and monsters during the fight against Shinra and Sephiroth. That could be considered 'evil', yet we know that he survived.