I guess you can hande this with a serverside plugin.
It can listen to the event when a user is created, do the necessary lookups and decide to what channels the new user should be added.
More info on writing plugins (it’s not that hard) you can find on my blog Introduction to Mattermost Plugins (part 4: webapp-plugins is still a work in progress)
Or the GitHub - mattermost/mattermost-plugin-welcomebot can help you as well?