Violence was no longer a taboo for the Buddhists: it was part of their strategy, together with sexual unruliness and a conscious resorting to social revolt. It is a mistake to consider the incitements to revolt contained in the texts and the manifestations of violence in both texts and iconographies as purely symbolic. They are literal and metaphorical, not symbolic. As metaphors, through the analogical process, texts and iconographies transfer the violence committed by the Buddhists on the tīrthika-s to those carried out on the Brahmanical gods by the new Buddhist deities. That a symbolic interpretation started developing at an early stage is not particularly significant, because it was largely the work of trans-Himalayan Buddhists who had to adapt the received tradition to a context where there were no tīrthika-s. The Vajrayāna was considered part of the true teaching of the Buddha, and neither texts nor images could be changed: they could only be interpreted. These interpretations have their own legitimacy, and so deep and influential as to have generated an entire symbolic universe, extending from Tibet to Japan, but we must first distinguish between Indian Buddhism and the violent world where it developed and the forms it took when it was received outside India.
Giovanni Veraridi, Hardships and Downfall of Buddhism in India (New Delhi, India: Manohar, 2011), 349-350.
Verardi's ideas are somewhat contentious as a lot of Indian scholars are reluctant to acknowledge the violence that occurred between Brahmans and Buddhists. I had tea with a certain eminent scholar not so long ago and he rejected Verardi's ideas outright.
Nevertheless, I think Verardi makes a compelling case.
There's also the point that Nālandā and other such monasteries became fortresses in the post-Gupta period (c.550 onward). Granted, fortresses are used for self-defence, but then at the same time it reveals it was a hostile world that existed, otherwise there would have been no need for such defences.
So did the violent iconography and literature of Vajrayāna have literal reality behind it? It would seem so, but then people might be reluctant to concede this. For ideological reasons Buddhists would not want to admit their predecessors ideologically sanctioned violence. However, this point is still up in the air.