Note:  I'm the EclipseLink JAXB (MOXy) lead and a member of the JAXB (JSR-222) expert group.
Below is how you could support this use case with MOXy as your JSON-binding provider.
Java Model
By default a JAXB implementation will convert a byte[] to base64Binary.  You can use the HexBinaryAdapter to have it represented as hexBinary.
package forum15643723;
import javax.xml.bind.annotation.*;
import javax.xml.bind.annotation.adapters.*;
@XmlAccessorType(XmlAccessType.FIELD)
public class Root {
    private byte[] foo;
    @XmlJavaTypeAdapter(HexBinaryAdapter.class)
    private byte[] bar;
}
Demo
In the demo code below we will read the JSON into objects and then write it back to JSON.
package forum15643723;
import java.util.*;
import javax.xml.bind.*;
import javax.xml.transform.stream.StreamSource;
import org.eclipse.persistence.jaxb.JAXBContextProperties;
public class Demo {
    public static void main(String[] args) throws Exception {
        Map<String, Object> properties = new HashMap<String, Object>();
        properties.put(JAXBContextProperties.MEDIA_TYPE, "application/json");
        properties.put(JAXBContextProperties.JSON_INCLUDE_ROOT, false);
        JAXBContext jc = JAXBContext.newInstance(new Class[] {Root.class}, properties);
        Unmarshaller unmarshaller = jc.createUnmarshaller();
        StreamSource json = new StreamSource("src/forum15643723/input.json");
        Root root = (Root) unmarshaller.unmarshal(json, Root.class).getValue();
        Marshaller marshaller = jc.createMarshaller();
        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
        marshaller.marshal(root, System.out);
    }
}
jaxb.properties
To specify MOXy as your JAXB provider you need to include a file called jaxb.properties in the same package as your domain model (see:  http://blog.bdoughan.com/2011/05/specifying-eclipselink-moxy-as-your.html).
javax.xml.bind.context.factory=org.eclipse.persistence.jaxb.JAXBContextFactory
input.json/Output
The foo and bar properties represent the same data.  foo is represented as base64Binary and bar is represented as hexBinary.
{
   "foo" : "3q2+78r+",
   "bar" : "DEADBEEFCAFE"
}
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