If you really only wish to assign permissions on user level, you can "fake" the roles table to make Shiro happy.
As Wouter mentioned, use the JdbcRealm
and specify the 3 queries for your table setup.
You should modify your permission table to have this structure:
permission (id, permissionname, user_fk)
Then you insert rows for the create_user/delete_user rights as needed.
This way it's very simple to add another permission (reset_password for example) to your setup, without the need to modify the db schema.
In the shiro.ini (or how you call the your shiro config file):
jdbcRealm = org.apache.shiro.realm.jdbc.JdbcRealm
For the queries use then this:
jdbcRealm.authenticationQuery = select password from user where email=?
jdbcRealm.userRolesQuery = select id from user where email=?
jdbcRealm.authenticationQuery = select permissionname from permission where user_fk=?
The small trick in your setup is: you don't have roles at all, so we just return the id of the user as the role name.
When the lookup in the permission table is done, it then uses the role name (=user pk) and returns the associated permissions.