Sorry for the late reply.

So far we worked around (or rather ignored for the time being) a part of the 
problem, but solved the other one.

The part we ignored so far is the programmatic configuration of EntityManagers. 
I understand that it is possible to achieve this by using the APIs Bill 
mentioned. For now we just stuck with the persistence.xml-based configuration 
of the EntityManager. We will, however, implement a solution for this part of 
the problem by implementing a custom EntityManager deployment/configuration 
solution. I'll happily share the solution once we've got it.

The second part of the problem was solved by adding an (EJB3-) interceptor 
which injects an EntityManager based on the realm mentioned in my initial 
posting. The EntityManagers per realm to be injected, however, still have to be 
configured via persistence.xml - our solution implements just a dynamic choice 
of the persistence context to be used on a call-by-call basis until the first 
part of the problem is solved.
To implement the dynamic EntityManager injection, a Bean has to be annotated 
with an interceptor. The interceptor scans the class for a field annotated with 
a second annotation which denotes the EntityManager field to be injected. Based 
on the caller principal the interceptor first identifies the realm, fetches the 
appropriate EntityManager from JNDI and finally injects the field.

Please let me know if there is interest in the details of this solution, I can 
post some details here or on the Wiki. 

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