Akon claims this is a "true" prisoner's dilemma situation, and then tries to add more values to one side of the scale. If he adds enough values to make cooperation higher value than defecting, then he was wrong to say it was a true prisoner's dilemma. But the story has made it clear that the aliens appear to be not smart enough to accurately anticipate human behaviour (or vice versa for that matter), so this is not a situation where it is rational to cooperate in a true prisoner's dilemma. If it really is a true prisoner's dilemma, they should just defect.

Of course, there may be a more humane approach than extermination or requiring them to live under human law: forcible modification to remove the desire to eat babies, and reduce the amount of reproduction. It might be a little tricky to do this without completely messing up the aliens' psychology.

Also, it seems a little unlikely that a third ship would arrive given that the arrival of even one alien ship was considered so surprising in the first installment.