Using groovy script like this:

import jenkins.model.*
import hudson.security.*
import hudson.plugins.active_directory.*

def instance = Jenkins.getInstance()
String domain = 'mydomain.com'
String site = null
String server = 'my_ldap_server'
String bindName = null
String bindPassword = null

adrealm = new ActiveDirectorySecurityRealm(domain, site, bindName, bindPassword, server)
instance.setSecurityRealm(adrealm)

instance.save()

field domain controllers remains empty. This was working in previous version of plugin and it's somehow related to multiple domain support.