No he didn't. He said "We love GitHub login. Your GitHub account is your developer identity, and many users are accustomed to signing into developer tools and services (e.g. Travis, Circle) with their GitHub accounts."
That leaves open the door for migrating all github accounts into Live accounts within a github namespace. The could have already done it but aren't letting it leak into the github UI yet.
>Use your GitHub account to sign into MS other services.
This isn't an argument they won't do it. It suggests that they will even more.
Implementing GitHub login for Microsoft's other products can be split into three categories of possibility:
1) Other MS services add support for GitHub's authentication systems.
2) GitHub accounts will be mirrored into Microsoft's existing account system.
3) GitHub's backend migrates to Microsoft's exiting account system.
The question isn't "if" but "when and with what UI" #3 will happen.
You don't have to go through 3 redirections to login, handling of 3rd party apps authorization is well thought out, and GitHub is already used an auth provider for many dev servcies, Microsoft accounts are not.
Pretty sure this will be the first change after the acquisition. Microsoft has to ease the path from checking in code to Github to building and deploying it on Azure.