2. I think you focused on the employee payoff matrix to argue that they'll always pick to defect. but I would argue that humans have "emotions" and sometimes even loyalty. like i said, I personally would have stayed the course and sacrificed some of my "payoff matrix" but never got the chance.
disclaimer: i may have again butchered the theory of prisoner's dilemma, but i think you get my point so hopefully we can avoid arguing the technicalities of prisoner's dilemma.
Lastly, I would argue that in startups, this is a game you do want to play over and over. if you're only hiring expendable, replaceable employees, then you're probably playing the wrong game, with the disclaimer that I definitely don't have all the answers and reserve the right to be wrong.