Meteor approaches Midgar, but is eliminated before it actually strikes the city. Nevertheless, the cyclones kicked up by its approach devastate Midgar and render it essentially uninhabitable. Advent Children -and- On the Way to a Smile SpoilersIn AC, a new city called Edge has been built on the outskirts of the ruined Midgar. Further, the mass exodus from Midgar is somewhat detailed in Kazushige Nojima's novella On the Way to a Smile, which helps bridge FFVII and AC. Even without looking to these sources, however, it's clear that Meteor never hits the surface of Gaia, as Midgar (though overgrown and abandoned) can still be seen 500 years later. Had Meteor struck the Planet, Midgar would have been annihilated beyond any recognition whatsoever.
EDIT: Lost Number, the mere existence of Advent Children and Dirge of Cerberus should completely clear up the misconception that Holy destroyed humanity. Obviously, it didn't.
Also, the wound would be located wherever Meteor struck, and the Lifestream would gather there to heal it regardless of the previous Spirit Energy concentration of the location.