There has always been a strain of utopianism in the study of ancient history that tries desperately to fit radically implausible social critiques into areas we are ignorant of.
It is the sociological or anthropological equivalent of the "God of the gaps" approach in the hard sciences, which disingenuously begs the question "Does God exist?" by insisting that anything we can't positively and fairly certainly explain by physical causes must be due to the Big Guy in the Sky.
In the case of magically peaceful civilizations, the most extreme instance was the Maya, who up until the last quarter of the 20th century were presumed to have "solved the problem of war", unlike we nasty brutish and short moderns. Then we learned to read their writing, and discovered they were incredibly violent and war-prone, just like every other human civilization: http://articles.sun-sentinel.com/1986-05-27/news/8601310832_...
The similarity between the article's claims about the Harappan civilization to the myths about the Maya are so striking that I've got to say the author and editor are both pretty far out of their depth to have not mentioned it.
So my prediction is that contrary to the article's closing complex question, we won't ever find out how the Harappan civilization avoided war, because they didn't. When their writing is eventually translated there will be the "surprising" revelation that their highly ordered civilization was heavily regulated by highly organized violence at all scales, just like every other one we know anything detailed about.
As a river civilization, state control of irrigation may have played a significant role in social control, but violence underpinned it, and warfare was the largest-scale expression of that violence. Lack of evidence of sacked cities is evidence that they didn't sack cities, not that they didn't engage in war. Maybe they simply killed all the inhabitants in a more organized way. They were, after all, highly organized.
In general, it is more likely that the gaps are filled with things similar to well-studied cases than completely and entirely at odds with them. These mysterious people are deeply fascinating and were clearly extremely accomplished, but the odds are they had basic sociological similarities to everyone else.