We are in the process of re-thinking our tech stack and below are our choices (We can\'t live without Spring and Hibernate due to the complexity etc of the app). We are also mov
JTA doesn't mean two phase commits. I think it's the combination of JTA and XA drivers that makes two phase commits possible.
I'd still recommend using JTA and declarative transactions over embedding transaction logic in code. Transactions are best done in aspect oriented fashion, a la Spring.
UPDATE:
With the additional information you've posted, I agree with your argument. I'd recommend using Spring declarative transactions and the HibernateTransactionManager class.