In case of web services JAXB doesn't come alone, but as data binding part of ws client framework. So I assume your question is how to use JAXB as data binding within axis 1.4. In general I think there is no easy way to achieve that, have a look at the following thread in axis-user mailing list: Specify JAXB generated complex types to Axis web service .
If the Axis side of the web service is also under you control then maybe you can set the property org.apache.axis.AxisEngine. PROP_DOMULTIREFS to false. In that case Axis shouldn't create multiRef elements.
I've used this property on client side Axis, hopefully it works on server side the same way.
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