I'm sure Calibre will be a handy tool, but I don't know if it will really make a huge difference. However I do see how some sort of content management system that is specifically designed for education will probably be a necessary component in educational ebook infrastructure.
Maybe Calibre or a derivative work could handle that, as a paid or service-supported add-on.
Of course, it may also be possible for an organization like Amazon to leverage its existing infrastructure for this task. E.g. the school's IT admin logs into a site, queues up certain texts to distribute to the users, and manages the email addresses associated with the devices.