A project I am working on uses Spring 2.5 & JPA with Hibernate as a provider.
My DAO classes extend JpaDaoSupport, so I get my JpaTemplate using the getJpaTempl
From an architectural point of view it is not a very good idea to let some other application bypass all your business logic and modify persistent data. It makes the ground beneath the feet of your application shaky in a lot of ways :)
Wouldn't it be a good idea to integrate with this other system in a more elegant way, for example by message processing or batch processing. Spring has great support for both of them.