In my case, I had a Spring Boot app where the majority of repositories were in one keyspace, and just two were in a second.  I kept the default Spring Boot configuration for the first keyspace, and manually configured the second keyspace using the same configuration approach Spring Boot uses for its autoconfiguration.
@Repository
@NoRepositoryBean // This uses a different keyspace than the default, so not auto-creating
public interface SecondKeyspaceTableARepository 
        extends MapIdCassandraRepository<SecondKeyspaceTableA> {
}
@Repository
@NoRepositoryBean // This uses a different keyspace than the default, so not auto-creating
public interface SecondKeyspaceTableBRepository
        extends MapIdCassandraRepository<SecondKeyspaceTableB> {
}
@Configuration
public class SecondKeyspaceCassandraConfig {
    public static final String KEYSPACE_NAME = "second_keyspace";
    /**
     * @see org.springframework.boot.autoconfigure.data.cassandra.CassandraDataAutoConfiguration#cassandraSession(CassandraConverter)
     */
    @Bean(autowireCandidate = false)
    public CassandraSessionFactoryBean secondKeyspaceCassandraSession(
            Cluster cluster, Environment environment, CassandraConverter converter) {
        CassandraSessionFactoryBean session = new CassandraSessionFactoryBean();
        session.setCluster(cluster);
        session.setConverter(converter);
        session.setKeyspaceName(KEYSPACE_NAME);
        Binder binder = Binder.get(environment);
        binder.bind("spring.data.cassandra.schema-action", SchemaAction.class)
                .ifBound(session::setSchemaAction);
        return session;
    }
    /**
     * @see org.springframework.boot.autoconfigure.data.cassandra.CassandraDataAutoConfiguration#cassandraTemplate(com.datastax.driver.core.Session, CassandraConverter)
     */
    @Bean(autowireCandidate = false)
    public CassandraTemplate secondKeyspaceCassandraTemplate(
            Cluster cluster, Environment environment, CassandraConverter converter) {
        return new CassandraTemplate(secondKeyspaceCassandraSession(cluster, environment, converter)
                .getObject(), converter);
    }
    @Bean
    public SecondKeyspaceTableARepository cdwEventRepository(
            Cluster cluster, Environment environment, CassandraConverter converter) {
        return createRepository(CDWEventRepository.class, 
                secondKeyspaceCassandraTemplate(cluster, environment, converter));
    }
    @Bean
    public SecondKeyspaceTableBTypeRepository dailyCapacityRepository(
            Cluster cluster, Environment environment, CassandraConverter converter) {
        return createRepository(DailyCapacityRepository.class,
                secondKeyspaceCassandraTemplate(cluster, environment, converter));
    }
    private <T> T createRepository(Class<T> repositoryInterface, CassandraTemplate operations) {
        return new CassandraRepositoryFactory(operations).getRepository(repositoryInterface);
    }
}