12.5% is still a significant percent of revenue.
With this change, Github foregoes a little revenue in exchange for securing the vast majority of their revenue.
It turned out to be damned easy (and very cheap) and that's a serious threat to github's future growth because once people start to default elsewhere for one type of their work, it tends to drag along other types of their work.
But, for one very obvious reason, people have grown more and more interested in finding alternatives to Github, and they're forced to compete.
Gitlab and Bitbucket both heavily positioned themselves against Github with their unlimited private repos feature. With this competing with Github is going to become much harder. I think it's a smart move for MS.