Ideally, that would be great. I doubt that would be an option though due to capacity. Would you rather stop/start your instance and risk a capacity error or have your impacted instances rebooted in 48 hours?
A reboot won't address it at all (it also keeps you on the same host).. no point in doing that. From the e-mail notification: "You will not be able to stop/start or re-launch instances in order to avoid this maintenance update."
This is not related to the scheduled reboot maintenance. The script that you are referring to has to do with a separate Windows networking driver and Xen.