Downloading email to your email client at home and not leaving on server, sort of defeats the needs of the many these days, having access to that same mail on every device, no matter where you're at.
Educating your users is helpful, but some users feel the need to save every single email, even deleted emails.
Reaching their email quota is an educational tool too, not just a nuisance.
Home »Server Configuration »Tweak Settings, Notifications tab, Mailbox disk quota options, can be adjusted. (or disabled)
Storage is storage, mail files or otherwise. When you run low, you get an alert and you've got to do something. Upgrade to a larger account so you can store more old email, or clean out some stuff to free up space.