In addition to using certificate-based with KeyVault, Azure Managed Service Identity also introduces a new way to make an Azure service become a service principal without any client app registration and client secret. Currently it is only available in preview stage for some services: Azure VM, Azure App Service, Azure Function, Azure Event Hub & Azure Service Bus. More information can be found here https://docs.microsoft.com/en-us/azure/active-directory/msi-overview
[Update] When ever you need to retrieve something from KeyVault, with Azure MSI you don't need a client secret. Only use AzureServiceTokenProvider()
method to retrieve access token
In real-world deployment with automation (for example via Ansible), you can use an external certificate to store sensitive variables in Ansibe Vault and generate a 256bit chain to secure such an info. During the automation deployment, the cert is decrypted to access to these variables and perform further deployment. This way adds more encryption layer to the whole Azure deployment.