I think you're not using the author's definition of "stupid" (an aggregate behavioral mode) but instead the more commonly understood meaning (lacking in intelligence or knowledge). I really don't want to be misquoted with an article of this nature, so I'm going to replace some terms in my response: "stupid" is now "destructive" and "intelligent" is now "generous."
The author's boldest thesis is that there are no common "destructive" characteristics outside of aggregate behavior. Only by looking at the net effect of an individual in question can you truly determine if their behavior is, to some degree, destructive. Or helpless. Or "bandit." Or generous. By the author's reasoning, "destructive" people cannot help but hurt others and to some extent themselves, regardless of all other factors except influence.
Mr. Cipolla's definition is firm, but adaptable enough to allow for all sorts of situations. What other social model is going to tell you up front that some Nobel laureates behave in destructive ways? That's not supposed to be allowed by the common metrics and understandings of the characteristic/success correlation model.
How many articles have you run across is the last, oh I don't know... year or so that can't seem to penetrate the "mystery" of why the best, brightest, most highly paid group of individuals in the world can't manage the very financial system that keeps them in business and the rest of us employed. Or why members of congress, with assured lives, cannot agree to measures which would enhance the well-being of themselves and their constituents. Or why unhappy, desperate people actively protest measures that would ease their suffering.
In each case you can point to specific reasons for these types of situations (incentives, irrationality, ignorance), but you haven't really said why these types of situations exist and continue to exist despite all of our other advancements. The author simply says that a group of people will experience decline as the balance of power shifts to the "destructive" members of that group, whoever they may be. The effects of this (in the author's mind) are clearly seen throughout history as a regular feature of humans, much as the male/female birth ratio has been unwavering.
What's fascinating about this essay is that it has to be the purest form of "don't judge a book by its cover" that I've ever read. It also agrees quite nicely (unless I'm mistaken) with the spirit of the Nash Equilibrium, which says that the best thing that you can do is take into account the other players' (members of society) potential actions and plan for the best outcome for yourself and all other players. According to Mr. Cipolla's model, the best thing you can do is elevate the generous (those who will help all) and mitigate the destructive (those who will hurt all), not just for yourself or in spite of them but for all of us.
I'm having a hard time disagreeing with that sentiment.