I don't understand how Microsoft, after having invested billions, doesn't have a board seat. If they did, I doubt this would've ever happened. I'm not sure why Microsoft let that happen.
But even ignoring that, the board making a decision as impactful as this without consulting their major investors is a dereliction of duty. That alone justifies getting rid of all of them because all of them are complicit in not consulting Microsoft (and probably others).
I have no idea why Sam was fired but it really feels just like an internal power struggle. Maybe there was genuine disagreement about the direction for the company but you choose a leader to make decisions. Ousting the CEO under vague descriptions of "communications with the board" just doesn't pass the smell test.
I'm reminded of this great line from Roger Sterling [1]:
> Half the time this business comes down to "I don't like this guy"
So much of working, performance reviews, hiring and firing decisions and promotions is completely vibes-based.
The fundamental thing you are missing here is that the charter of the non-profit and structure of their ownership of the for-profit (and the for-profit's operating agreement) is all designed in a way that is supposed to eliminate financial incentives for stakeholders as being the thing that the company and non-profit are beholden to.
It may turn out that the practical reality is different from the intent, but everything you're talking about was a feature and not a bug of how this whole thing was set up.