Deleting a sourceControlConfiguration will not result in deletion of the components that Flux v1 deployed based on the k8s manifests in the git repo. One option, when installing sourceControlConfiguration you can use the --sync-garbage-collection parameter to instruct Flux to remove any deployed component that has been removed from the git repo. With this, if you want to remove all deployed components from the k8s cluster components, you should be able to move the manifest files in the git repo to a location that is not accessible to Flux, and when Flux next reconciles it should remove the previously deployed components. Then you can delete the sourceControlConfiguration.
We are working on integrating Flux v2, which will have a simpler option.