They're cities were built primarily on the banks of an ancient river,
seems geologic activity in the Himalaya's changed the course of the river, throw in a sprinkle of climate change and no water = no life, there were a few exposed bodies found, but not like you'd expect after a massacre.
Anyone ever looked at the Aryan Invasion (migration) theory, it's basis lies in linguistic studies, the Indian's hate it as it suggests the origin of the Rg Veda is outside of India, basically it looks at the parallels between the Rg Veda & the Avesta the ancient Zoroastrian (Iran) script and suggests both came from central Asia possibly near the black sea.
I just kind of instinctively hate on every attempt to reconstruct or understand extinct civilizations- even when dealing with contemporary foreign peoples, everyone has a tendency to collective their opinion of them and to confuse their outward, public behavior with their inner life, as though saluting a flag say implies an actual psychological dedication to it- maybe they are just afraid to look weird to their neighbors, who are afraid to look like traitors to a small and insane minority political class, for example.
I did a project on Harappan civilization for an archaeology class. I thought it was very interesting how they created something that we would instantly recognize as a complex urban society, but it was so different from how we do things. A lot of scholars focus on Harappan social/administrative structure because there's no real evidence of a centralized government or ruling class. Some take the absence of evidence to be the evidence of absence and insist that the Harappans were an egalitarian and peaceful society - then I started reading about the "massacre pits." They're actually not uncommon in Harappan cities, but they often get ignored because, regardless of their function, their existence implies that the Harappans were capable of great violence (just like everyone else). It still surprises me how easily people forget that ancient people were just like us.
Just stumbled across the full paper, interesting read, looking at social stratification through cemetary burials and number of injuries. They had nice neat cities, but still killed each other.
[url=http://www.academia.edu/2080193/A_Peaceful_Realm_Trauma_and_social_differentiation_at_Harappa]A Peaceful Realm? Trauma and social differentiation at Harappa | Gwen Robbins Schug - Academia.edu[/url]
The burial pit outside the city walls where bodies were thrown in without regard or ritual and the odd dog thrown in, are they the massacre pits you refer to.