我最终得到了AOP解决方案：

@Aspect
@Component
public class EnableFilterAspect {

    @AfterReturning(
            pointcut="bean(entityManagerFactory) && execution(* createEntityManager(..))",
            returning="retVal")
    public void getSessionAfter(JoinPoint joinPoint, Object retVal) {
        if (retVal != null && EntityManager.class.isInstance(retVal)) {
            Session session = ((EntityManager) retVal).unwrap(Session.class);
            session.enableFilter("myFilter").setParameter("myParameter", "myValue");
        }
    }

}