Problemi con @Qualifier

Prova questo:

public class MongoDbConfig {
    @Bean(name = {"sourceTemplate", "mongoTemplate"})
    public MongoTemplate getSourceTemplate() {
        MongoTemplate mt = new MongoTemplate(getMongoDbFactory(sourceServers, sourceDatabaseName));
        return mt;
    }

    @Bean(name="destinationTemplate")
    public MongoTemplate getDestinationTemplate() {
        MongoTemplate mt = new MongoTemplate(getMongoDbFactory(destinationServers, destinationDatabaseName));
        return mt;
    }
}

public class SourceDaoImpl implements SourceDao {
    @Autowired
    @Qualifier("sourceTemplate")
    private MongoOperations mongoOps;
}


public class DestinationDaoImpl implements DestinationDao {
    @Autowired
    @Qualifier("destinationTemplate")
    private MongoOperations mongoOps;
}

Aggiornato

In realtà il metodo:

@Bean
    @ConditionalOnMissingBean
    public GridFsTemplate gridFsTemplate(MongoDbFactory mongoDbFactory,
            MongoTemplate mongoTemplate) {
        return new GridFsTemplate(
                new GridFsMongoDbFactory(mongoDbFactory, this.properties),
                mongoTemplate.getConverter());
    }

in MongoDataAutoConfiguration richiede un bean di MongoTemplate di nome "mongoTemplate", che non può essere trovato, invece hai definito i tuoi altri 2 bean "sourceTemplate" e "destinationTemplate".

Penso che questo risolverà il tuo problema!