If you have source control configured with your application, the webjobs should be deployed as part of the source control integration.
Form App Service perspective a webjob is just part of the content of the app.
If you deploy a webjob through the portal (before we added the restriction to block it) and then had a commit to your source control, then the webjob would be removed since it wasn't part of the payload being published by source control.
The right way to do this is to make sure webjobs are part of your solution.
As a workaround, you can deploy webjobs through FTP/FTPS but keep in mind they will be removed the moment source control does the next deployment.