I have a class and a joined sub-class that have independent primary keys, both of which I'd like to generate from Oracle sequences.

Using Oracle to generate the key for the class is no problem, since I can use the <id> element at the class level to declare the primary key column of the table, and use the <generator> child element to specify that Oracle will handle the sequence.

So far as I can tell, however, I cannot do the same thing for the joined sub-class, since the sub-class does not permit a nested <id> element.

Is there a way to tell hibernate to allow Oracle to generate different keys using differenct sequences for a class and its joined sub-class?

No. Hibernate assumes a primary key association between the tables.