If you're building a database agnostic application and not using any of the inherent features of a specific database vendor, then the scope of your test cases should be to test the setup, manipulation, and accessing of the data through the DAO objects and less with the testing of the actual database backend. Hibernate 3.5 has dialects available for both Oracle 11g and DB2, so if you were writing test cases that tested the integration of the database agnostic application with a specific database vendor, then really what you are doing is testing that the hibernate dialects do as they say they do (which I'm sure has been covered by test cases in the hibernate project).
In other words, in your case I would think that the testing should focus more on the DAO retrieving the data that you think that it will retrieve after you've set that data up, and in-memory databases are fine for that.
Now all that said, both DB2 and Oracle have very good documentation related to setup. Indeed, both of them have "wizards" to do that. If you still think that it's prudent to test adding data to the database and retrieving it from the physical, non-in-memory database, then I would recommend setting up a "test database" environment and pointing your datasource to that during your continuous integration tests. If you're using Hudson or Jenkins for CI, you can set it up to run a script after the build completes that will truncate the database tables so that the next round of tests work from a blank slate.
EDIT:
I just saw the updates that you posted to your question, so let me address them. Since you already have the databases setup and configured then what you really want to do is dynamically select what the database should be. One way to do this would be to setup your datasource using System properties that can be inherited from a properties file, and running your tests in a "DB2-test" environment and an "Oracle-test" environment. Using this method, you'll have to setup the datasource programmatically and have it read system environment variables to determine which database it connects to. This would essentially require you to change your CI script to run the DB2-test environment first, then the Oracle-test environment following that -- your test suites will run twice.
Hope this helps!