Yeah, but they weren't directly hurting the planet. Nothing Sephiroth or Jenova or them could do would directly hurt the Planet. Sure, they could hurt the life on the Planet, but not the Planet itself.

Meteor had the power to do that, however.
So, new theory: the Weapons were confused. They knew there was a threat, but they couldn't find it('cause it was miles above them). So they went rampaging across the earth, trying to find it. Stupid, confused Weapons.

Ah, well, I tried. heh