We use the wp-cli with cron jobs such as indexing when we post with API or database-related things. Even with wp-cli we must login to SSH individually. And this doesn't give us the wp-cli option since it is 3rd party zip file. We possibly can get the file, extract, and delete the old plugin with cli, and then enable the last updated plugin with with cli again with a script. Either way, we must create a script or suck it up, go into each wp individually, and take care of it from the backend...