if you run out of time the round is negated (both players score 0 points)

In the OP, defect/defect gives each player one point. Did you intend to add a fifth possible outcome for each iteration?

I think a more natural expansion would be to have a third choice besides cooperate and defect lead to nine different possible scores per iteration. For a program to run out of time is a choice pre-committed to by the design of the analyzing function, it's not too different from the outcomes of cooperate or defect.