The non-profit is legally obligated to follow their charter. If they truly believe that allowing Altman to remain CEO is a contraindication to that, then they have to fire him. They might not survive such a firing due to the fallout, but that doesn't matter - if one option is assured movement away from their charter and the other is potential destruction while still adhering to it, the latter is still the correct choice.
The non-profit will not exist at all if Microsoft walks away and all the other investors follow Sam and Greg. Neither GPUs nor researchers are free.