Furthermore, this study is definitely flawed since it's quite obvious that individual intelligence has done a great deal lot more good for society than bad. Is there even an argument about this?

The study itself isn't modelling all aspects of society, just a very limited set of PD situations. That society has on the whole benefited from intelligence is due primarily to inventions and discoveries, which have no analog in PD, Maybe if one had a version where the more previous rounds of cooperation there have been the higher then payoff of cooperation in future rounds one might have something that approached that.