There's nothing about Khan Academy's application (or any other customer's) that would somehow immunize it from platform-wide serving issues.
But you can bet that if Khan Academy has a problem it will be looked into with extra attention.
Also, Khan academy receives funding from Google ( http://en.wikipedia.org/wiki/Khan_academy ), so I don't think it boils down to only having a Premier account.
Whether you believe it or not, a Premier account is what you need if you want support. You could argue that $500/mo is too expensive, but it is what it is.
What I don't believe is that the support provided by Google is good or sufficient. Based on experiences with paying Google Apps, I'd say it's not.