Mohanjodaro (Moyan-jo-dero, I always want to put it like that, Mohanjodaro linguistically does not make any sense), was a trading town like Lothal. Trade in the East dwindled for some reason and that in West increased, Rakhigarhi, Kalibangan, etc. That I think is the reason for decline of Moyan-jo-dero, added perhaps by a pestilence (the 40 skeletons), and the city never recovered. Not any violence, IMHO.
Thus, it seems to me that we must consider the end of Mohenjo-Daro from a more panoramic view, carefully examining its relations with the other IVC centres and with foreign powers, as well as the gradual drying up of Saraswati which might have provoked the universal decline of the Indus-Saraswati Civilization. All of the IVC sites shared extremely similar cultural manifestations; they may have been ruled from one centre, and thus, what affected one city would unavoidably have affected the others. Especially if Saraswati, and not Indus, had been the sacred river of this civilization.