What is the economic incentive to cheat? How does an experiment capture exogenous deviations?
A couple of comments to your question below:


  When an economic experiment is designed to have predetermined outcomes of ethical and unethical decisions, how does it address the extreme levels of deviation that is present within historical record?


1) External validity --- whether results obtained in the lab can be generalized to settings outside the lab --- has long been one of the main criticisms of experimental economics, and practitioners in this field are well aware of this. In light of this concern, one must therefore exercise caution in interpreting experimental results. Lab results should be extrapolated to an external environment only if the settings of the experiment sufficiently resemble those in that environment. (To some extent, the same can be said about generalizations of results obtained using field data.)

In the experiment that you participated, decisions were labeled as "cooperate" and "cheat". However, the labels could very well be "A" and "B", or "Left" and "Right", or "Aspiring" and "Cautious". The point is that the labeling of the actions is arbitrary, and you shouldn't (over)interpret the results just because the experimenter happen to choose a non-neutral frame. 

2) Judging by your very limited description of the experiment --- e.g. you didn't say what the control treatment was like, or whether the subject moving at stage 2 can observe what was chosen in stage 1 --- I suspect that the experiment was more for a pedagogical purpose than a research one. Generally speaking, experiments for research purposes should avoid recruiting subjects from the experimenter's own class, since there are strong outside incentives that may affect/dominate the salience of the payoff from within the experiment. Moreover, experiments should generally adopt neutral framing, since non-neutral frames tend to bias the results in a certain direction. 

Therefore, I think you are over-interpreting the results in an experiment that is not very rigorously conducted.