Lea BSON (mongoDB) en POJO usando GSON y TypeAdapter

Lo resolví usando una fábrica de adaptadores de tipo personalizados. Ver esta pregunta

Básicamente, primero escribe un adaptador personalizado:

public abstract class CustomizedTypeAdapterFactory<C>
        implements TypeAdapterFactory
{
    private final Class<C> customizedClass;

    public CustomizedTypeAdapterFactory(Class<C> customizedClass) {
        this.customizedClass = customizedClass;
    }

    @SuppressWarnings("unchecked") // we use a runtime check to guarantee that 'C' and 'T' are equal
    public final <T> TypeAdapter<T> create(Gson gson, TypeToken<T> type) {
        return type.getRawType() == customizedClass
                ? (TypeAdapter<T>) customizeMyClassAdapter(gson, (TypeToken<C>) type)
                : null;
    }

    private TypeAdapter<C> customizeMyClassAdapter(Gson gson, TypeToken<C> type) {
        final TypeAdapter<C> delegate = gson.getDelegateAdapter(this, type);
        final TypeAdapter<JsonElement> elementAdapter = gson.getAdapter(JsonElement.class);
        return new TypeAdapter<C>() {
            @Override public void write(JsonWriter out, C value) throws IOException
            {
                JsonElement tree = delegate.toJsonTree(value);
                beforeWrite(value, tree);
                elementAdapter.write(out, tree);
            }
            @Override public C read(JsonReader in) throws IOException {
                JsonElement tree = elementAdapter.read(in);
                afterRead(tree);
                return delegate.fromJsonTree(tree);
            }
        };
    }

    /**
     * Override this to muck with {@code toSerialize} before it is written to
     * the outgoing JSON stream.
     */
    protected void beforeWrite(C source, JsonElement toSerialize) {
    }

    /**
     * Override this to muck with {@code deserialized} before it parsed into
     * the application type.
     */
    protected void afterRead(JsonElement deserialized) {
    }
}

Y luego cree una subclase para todas las clases que deben tenerse en cuenta. Tienes que crear uno para cada clase que contenga un largo (en este caso). Pero no tiene que serializar nada más que el valor largo (y cualquier otro valor específico de bson)

public class MyTestObjectTypeAdapterFactory extends CustomizedTypeAdapterFactory<MyTestObject>
{
    public MyTestObjectTypeAdapterFactory()
    {
        super(MyTestObject.class);
    }

    @Override
    protected void beforeWrite(MyTestObject source, JsonElement toSerialize)
    {
        //you could convert back the other way here, I let mongo's document parser take care of that.
    }

    @Override
    protected void afterRead(JsonElement deserialized)
    {
        JsonObject timestamp = deserialized.getAsJsonObject().get("timestamp").getAsJsonObject();
        deserialized.getAsJsonObject().remove("timestamp");
        deserialized.getAsJsonObject().add("timestamp",timestamp.get("$numberLong"));
    }
}

y luego generar Gson con:

Gson gson = new GsonBuilder().registerTypeAdapterFactory(new MyTestObjectTypeAdapterFactory()).create();