Is there a way to automatically activate repositories as soon as they are created on github organization?
This functionality is not built-in to Drone but you can enhance Drone using its API. For example, you could create a small micro-service that receives organization webhooks  from GitHub, and then use the Drone API  to sync the repository list and activate  the repository.
What is the endpoint for syncing the repository list?
Sorry, forgot to include the link. Use https://docs.drone.io/api/user/user_sync/
It usually works but sometimes, I have to wait a couple of seconds before repo activation succeeds.