If a situation arises where Gatekeeper is preventing the cluster from operating correctly, the webhook can be disabled. This will remove all Gatekeeper admission checks. Assuming the default webhook name has been used this can be achieved by running:
kubectl delete validatingwebhookconfigurations.admissionregistration.k8s.io gatekeeper-validating-webhook-configuration
Redeploying the webhook configuration will re-enable Gatekeeper.