Well, obviously the result depends on what the algorithms actually do. If you're going to be playing against an opponent with access to your source code, you'd quite like to be a nice simple "always-stand-firm" program, which even a very stupid opponent can prove will not flinch. But of course that leads to all algorithms doing that, and then everybody dies.
It's not clear that this is avoidable. While it's interesting to think in the abstract about programs analysing one another's code, I think that in practice programs clever enough to do anything nontrivial with one another's code are almost inevitably much too difficult to analyse, and unless there are big disparities in computational resource available simulation isn't much help either. So we're left with doing trivial things with one another's code: e.g., perhaps you could say "if facing an exact copy of myself, flinch with probability p; else stand firm unconditionally", and anything that makes a halfway-serious attempt at analysis will see that it isn't going to win. (What's the best value of p? Depends on the exact payoffs. With classical Chicken where "neither flinch" => "both die", it's probably very close to 1. But then with classical Chicken the best meta-algorithm is not to play the damn game in the first place.)
Suppose that Red got to move first. There are some games where moving first is terrible - take Rock Paper Scissors for example. But in this game, moving first is great, because you get to narrow down your opponent's options! If Red goes first, Red picks 'A', and then Blue has to pick 'B' to get a cookie.
This is basically kidnapping. Red has taken all three cookies hostage, and nobody gets any cookies unless Blue agrees to Red's demands for two cookies. Whoever gets to move first plays the kidnapper, and the other player has to decide whether to accede to their ransom demand in exchange for a cookie.
What if neither player gets to move before the other, but instead they have their moves revealed at the same time?
Pre-Move Chat:
Red: "I'm going to pick A, you'd better pick B."
Blue: "I don't care what you pick, I'm picking A. You can pick A too if you really want to get 0 cookies."
Red: "Okay I'm really seriously going to pick A. Please pick B."
Blue: "Nah, don't think so. I'll just pick A. You should just pick B."
And so on. They are now playing a game of Chicken. Whoever swerves first is worse off, but if neither of them give in, they crash into each other and die and get no cookies.
So, The Question: is it better to play A, or to play B?