It's not necessary to use Ebean, I have used mybatis as persistence provider, but in order to save the user and login without problem you should use the same hashing algorithm.
the hashing algorithm is used to store the password.
to use your custom persistence provider like JPA or whatever you want, you should implement the Authentication Provider interfaces, see UsernamePasswordAuthProvider in the example project for more details.
Focus ,especially, on "signupUser" and "loginUser" methods.
I have modified play-authenticate to support Login/password instead of email/password identityId.
see Modified version of Play-Authenticate.
Cheers.