I have only skimmed the memo, so I may be missing something, but calling this an "ultimatum" and saying things like "adopt holacracy or leave" seems awfully overdramatic. If a CEO says "Hey, we're rearranging the org chart now," and you can't can't bear the thought of working under the new org chart, then unless you're in a position to talk him out of it, your only real option is to quit. Nobody has to mention the option explicitly; it's understood. That's not an "ultimatum," it's what being an employee means.
This guy is explicitly bringing it up because he's offering extra benefits to anyone who chooses to quit. He's being more accommodating than the average CEO, not less.