It seems like as long as the complexity of the passphrase is sufficient, then a rainbow table can't be effective. For example, a 128-bit random AES key is a kind of passphrase that's generally not susceptible to a rainbow table attack (though it's very hard for humans to remember). So the problem here is, how do you force the user to make their passphrase sufficiently complex?

Passphrases also don't protect against keyloggers, which is a downside of this approach.