The javadoc for Jaxb2Marshaller makes no mention of thread-safety one way or another, so I'm not sure why you think it's not. If it wasn't thread-safe, the javadoc would say that very clearly.
Create several of them (say five), put them into a pool (a queue) and when a thread needs one, it removes it from the pool. When the pool is empty, a few threads will have to wait for the active threads to complete their work and return the marshaller.
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