Even if you interpret the second one as "new buttons to advertise Microsoft products", it doesn't damage a developer-first stance or independent operation.
Moreover, GitHub has already partnered with dozens of other companies for its Education program for instance [0]. This already compromises independent operation, and displays ads to thousands of students, "whether or not they like these tools" (your words).
MS will integrate Github with MS Ecosystem ( Azure , .NET , VSTS etc.. ) as described in their slides.
From this point there is two possibility
A - They open every single new API they use as well as UI/UX API so other providers can integrate themself to Github
B - They don't open (or partially) those new API and Azure/MS Ecosystem will be the de facto providers for every single stuff that is possible in github. You will end up with a "Open in [Insert Microsoft Products]" buttons and you won't be able to change that , third party providers won't be able to appear here as well. Github would have never done in the first place because they were independant , now every single stuff they do will have to be linked one way or another to MS.
Even if you interpret the second one as "new buttons to advertise Microsoft products", it doesn't damage a developer-first stance or independent operation.
Moreover, GitHub has already partnered with dozens of other companies for its Education program for instance [0]. This already compromises independent operation, and displays ads to thousands of students, "whether or not they like these tools" (your words).
[0] - https://education.github.com/