if Github was running out of money
Then MS's involvement is a bit less toxic. The Ars commentards for one seem fairly down with it. Part of it is the sheer lack of less toxic suitors - Oracle or IBM, for example? Google and Apple are not obviously much better. FB and Amazon even less so.
There is even one potential upside, which is that, done well, this could really give open source credibility in stodgy ol' Enterprisey companies that have never looked at open source. I.e. it could open a lot of doors to suits that perceive open source as the domain of hippies and beardies, if they're aware of it at all.
But, yes, if MS screws that up, and on past record it would not be an unreasonable expectation for them to do so, then they will have done that very publicly and alienated a core constituency.
The less they do and the more they lay low for the next year or so, the better.
Be lazy. Don't change things.
Don't change them "the MS way". Don't monetize openly on the site. Don't telemetrize. Under promise, over deliver. Put necklace bombs around your rah-rah marketing and PR people and have them set to blow up if they go anywhere near the site. Shoot anyone who thinks of automating LinkedIn integration.
You need to commit, very strongly, and with the appointment of an internal ombudsman and external auditors, that private repos will not be accessible by MS at large and will only be looked at when required to support customers. OK, sensible companies with any possible competition w you will flee anyway, but at least it will show you understand the issue and respect your users.
Pick a few long hurting problem areas identified as needing improvement by the community and try fixing them.
Given that "security and MS" often rhymes with "security and Adobe", and that Github repo poisoning has been a potential issue in the past, be doubly careful - you don't want to reinforce negative associations here. Time to invest in maybe some predictive analytics/machine learning to flag things like typo squatting.
Sounds ungrateful to someone who just overpaid to the tune of $7.5B, but that's now your shareholders' problem, not ours. Remember that many people expect you to fail and it will be visible enough that you want to think 3 times before doing your business as usual.