Hi,
personally I don't see a problem there. If you are sticking with JPA annotations all you need to include for your clients is the javax.persistence jar. You don't have to include the actual Hibernate runtime dependencies. I think that is a fair price for a more compact and easier to maintain meta data configuration.
Maybe this thread is also of interest for you:
http://forum.hibernate.org/viewtopic.php?p=2391258.
However, the whole discussion is certainly a little bit of a religious one, similar to database design and many other design questions. I am sure there many developers out there who would consider using annotations in this case as 'not clean'.
I don't think there is a definite right or wrong answer to your questions. Sorry :)
--Hardy