The problem here is partially the word 'wrapper', partially a false dichotomy, and partially a false distinction between the JDK and everything else.
The word 'wrapper'
Wrapping all of Hibernate, as you say, is a completely impractical enterprise.
Restricting the Hibernate dependencies to an identified, controlled, set of source files, on the other hand, may well be practical and achieve the same results.
The false dichotomy
The false dichotomy is the failure to recognize a third option: standards. If you use, say, JPA annotations, you can swap Hibernate for other things. If you are writing a web service and use JAX-WS annotations and JAX-B, you can swap between the JDK, CXF, Glassfish, or whatever.
The false distinction
Sure, the JDK changes slowly and is unlikely to die. But major open source packages also change slowly and are unlikely to die. Untold thousands of developers and projects use Hibernate. There's really no more risk of Hibernate disappearing or making radical incompatible API changes than there is of Java itself.