Just remove username@domain from username option

To prevent your customers encountering problems down the road as explained in your FAQ (FAQ Q10: What's the deal with @ in mailbox usernames?)... why not just remove username@domain option from > Sever Template > Mail for domain ?

Also include a javascript pop-up warning if someone enters @ in the username field.

Nothing good can come out of providing that option in Server Template. Just remove it for simplicity sake. If someone definitely wants to use @ in the username, they can enter it via username field.