I believe you're making two assumptions, one of which is untrue, and the other isn't necessarily true.
The first being that it's a better indicator of independence to have no CEO than a Microsoft appointed CEO. The number of good CEOs that have experience running companies with hundred-million valuations is very low, as GitHub themselves experienced for months. Without a good CEO, chances are GitHub goes under (somebody needs to push the Azure integration, etc.), so Microsoft didn't really have a choice.
The second assumption is that Nat will necessarily run GitHub from a Microsoft-first perspective, as opposed to a GitHub-first perspective. This may be true, and it may not. I believe this is what they were referring to with regards to "independence".
Please clarify if you're not making either of those assumptions, and if you are, I'm happy to discuss your justifications. :)
Edit: Perhaps you just have a feeling, given Microsoft's history, that they will sink the boat, and you're trying to justify it through anything that you can find that is concrete. Personally I don't believe that GitHub will stay a completely neutral shrine of perfection, and my only justification is my feelings based on history. So if that is the case, I completely agree. The idea of appointing a CEO where there is none being non-independent, though, is clutching straws IMO.