Any valid email addresses can be used to login to Khan Academy. Refer to our Coach Resources article on Setting up accounts for more information.
If you are looking to setup accounts for an entire school of district of students, you may also want to consider using Clever, which enables syncing of your rosters for free.
A note about Google Apps for Education: This is a free offering for public and other nonprofit schools (most charter and independent schools are covered under this). With Google Apps for Education, you can set up Google Accounts under your own domain name (e.g., lasdk8.org) and create accounts for students, even if they are under age 13. You can choose to enable or disable features such as email on these accounts.You can use these Google Accounts to login to Khan Academy as well. Check out Google's information at http://www.google.com/apps/intl/en/edu/k12.html for more information on Apps for Education.