Drone is a useful Open Source CI Server. You can host the private and dedicate CI environement.
Once you delete or modify the webhooks on the github (enterprise), never reset the setting from Web UI. NOT YET IMPLEMENTED.
But, we have APIs.
First of all, get the api key from https://your.ci.server/account/profile
$ curl -X POST https://your.ci.server/api/repos/github.com/ashphy/baku?access_token=<INSERT YOUR API KEY>
API Reference: http://readme.drone.io/api/repos/post/
Deactivate is also available.