More than an year old thread. When I googled for "hibernate update generates additional comma", I got this as the first result. Hence thought of updating my experience. For me, even getSession().createQuery(hql).executeUpdate() doesn't work. (I am still at 3.2.6.ga). With further luck, I came across this Hibernate (non)issue. Hope this is useful to someone.
subject: Hibernate generates "bad" SQL in Bulk update