I too have been struggling for a few days with how to start Hibernate. Situation was the same as yours, all four bundles were installed, but entity manager wasn't resolved. Today I changed karaf.framework setting from equinox to felix and it just started. I know it may not be an option for you, but at least it's a try. Version was 4.3.1-fuse-01-22 running on Linux.
Before that I was trying to find what's wrong with Hibernate. I even found out that both entity manager and hibernate itself export package org.hibernate.engine, but in two different versions. But then I downloaded FuseESB version 4.4.1, tried that and it worked. So I checked differences between Hibernate JARs, but they were identical.
Also, strange thing is that when I try to forcefully resolve entity manager's bundle I see nothing in logs, even if I set them to debug, Karaf seems to be ignoring me. I get no bundle resolved nor error message.