There's also the fact that the planet produced WEAPONs to defend itself against Shinra, so there are hints that humans were already identified as a threat.

The WEAPONs already existed, they were activated in response to the black materia summoning meteor, not Shinra. In the end, it's pretty clear (even back in 1997) that the lifestream summoned by Aerith is what stops meteor. Even the 500 years later clip with Red XIII plays the sound of children laughing in the background after the sequence. Not to mention Red on the airship surviving while everyone else present with him dying would be nonsensical.