Most of the time a website with an unmapped domain (subdomain.domain.com) is still in development. Unfortunately, Google will still index these sites if search engine visibility isn't disabled on the Settings > Readings page. This WordPress search engine setting is powerful because it automatically disables pings, adds disallow in robots.txt, adds no index/nofollow, in the header and more.
Using Pro Sites this is too tedious to manage manually due to the number of sites. It's also risky because if you forget to turn it off you end up disabling search engines on a live site, which is bad for business.
A simple fix would be hooking into the search engine disability setting on the Reading page and adding a setting in the Domain Mapping network page with a check box saying the below:
Search Engine Visibility: [ ] Discourage search engines from indexing sites without a mapped domain
Leaving this box unchecked would have no effect. But checking this box would tie the search engine settings to domain mapping on each site. So, when this option is enabled any website without a mapped domain would discourage search engines. Any site with a mapped domain would allow search engine robots as normal.
This would eliminate the issue of large swathes of development sites being indexed. The issue is that even months after a domain is mapped, Google still has pages with the subdomain address indexed. The only way to correct it is to do it manually in Webmaster Tools, which is tedious. By reducing the number of junk sites indexed from a network, the network's quality ranking will increase.