The Weapons aren't smart, they have no direct controller. They sensed a threat: Meteor. Jenova was insignificant by comparison.
I repeat: Sephiroth and Jenova can not directly harm the Planet, or only very little, at most. Meteor could. The Weapons sensed a dire threat, and rampaged around the Planet searching for it. They did not go looking for Jenova because she could not do anything against the Planet. Neither could Sephiroth.
