If they are merely yielding to market forces, then that's not much of a comfort. Github was a leader in this, and Microsoft's customers have a strong bias toward followers and laggards.
With Microsoft, the bites have been numerous and some are ongoing.
I completely agree with that as a general principle, and I don't disagree with anything you've said outside of this quote. But are you suggesting that Nadella is going to leave Microsoft anytime soon?
Github was making over $200m/year, and was poised for strong growth in enterprises as they got with the times. I expect they could have gotten to GAAP profitability whenever they needed to. But they should have kept spending on growth to maximize market share.
The only way that you guard against being an acquisition target is to remain private and not take money from outside investors.
Moreover, although I agree Microsoft is making efforts to change [1], pro-Microsoft partisans make it clear much of this is due to the new CEO. What one CEO does, another can undo. GitHub's bus factor is now 1.
I would much rather have seen them go public. They were losing money, but not, last I saw, at a rate that was absurd for building a SaaS business. Is there some reason to think they couldn't have gotten into the black? And if so, is there some reason to think Microsoft will let them burn cash forever without getting anything valuable in return?
Previously, GitHub's success depended on GitHub serving their customers and users. Now it depends on the notions of some guy in Seattle. Some guy whose job is, at least by market cap, 99% focused on other things. It's reasonable for customers to worry about that.