Best practice for configuring Spring LdapTemplate via annotations instead of XML?

Why all the subclasses? Just use configuration to configure the beans. Either XML or Java Config.

@Configuration
public class LdapConfiguration {

    @Autowired
    Environment env;

    @Bean
    public LdapContextSource contextSource () {
        LdapContextSource contextSource= new LdapContextSource();
        contextSource.setUrl(env.getRequiredProperty("ldap.url"));
        contextSource.setBase(env.getRequiredProperty("ldap.base"));
        contextSource.setUserDn(env.getRequiredProperty("ldap.user"));
        contextSource.setPassword(env.getRequiredProperty("ldap.password"));
        return contextSource;
    }

    @Bean
    public LdapTemplate ldapTemplate() {
        return new LdapTemplate(contextSource());        
    }

}

Your DirectoryService can remain the same as it will have the LdapTemplate autowired.

A general rule of thumb is that you don’t want to extend your infrastructure beans (like DataSource or LdapTemplate) but configure them explicitly. This as opposed to your application beans (services, repositories etc.).