After reviewing Microsoft's official documentation, it appears that Intune does not provide a built-in method to remove or revoke deployed web apps (web links) from iOS devices once they have been installed. The "Remove apps and configurations from devices" feature allows administrators to uninstall applications or remove configuration profiles from devices; however, this functionality is not applicable to web apps deployed via Intune. Microsoft Learn
Therefore, the most effective approach remains to instruct users to manually remove the web app from their devices. While this may not be the most efficient solution, it is currently the recommended method until Microsoft addresses this limitation in future updates.Reference