Well, their big mistake was being unwilling to be clear and explicit about this, but as I read it, the board's problem with him was that he wasn't actually acting as the executive of the non-profit that he was meant to be the executive of, but rather was acting entirely in the interests of a for-profit subsidiary of it (and in his own interests), which were in conflict with the non-profit's charter.
I think where they really screwed up was in being unwilling or unable to argue this case.
i'm still not clear what the accusation against Altman was... something about being cavalier about safety? if that was the claim and it has merit, i don't understand why it wasn't right to oust him, and why the employees are clamoring for him back