It doesn't completely stop working; a MITM can still pretend to be the server, it just can't authenticate to the real server on your behalf. You could be doing all your work in a fake server controlled by the attacker, while the real server sits there untouched.
If the attacker can get the cloud-init user-data while the script is still running (in the time between sending the cloud-config.yaml and connecting with SSH to the machine) that would still allow MitM, but would require more effort on the attacker's part to leak the cloud-init data.
The point of the script was that leaking the cloud-init data after the script has completed is harmless.