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[M]osques in Mughal India, though religiously potent, were considered detached from both sovereign terrain and dynastic authority, and hence politically inactive. As such, their desecration would have no relevance to the business of disestablishing a regime that had patronised them. Not surprisingly, then, when Hindu rulers established their authority over the territories of defeated Muslim rulers, they did not as a rule desecrate mosques or shrines, as, for example, when Shivaji established a Maratha kingdom on the ashes of Bijapur's former dominions of Maharashtra, or when Vijayanagara annexed the former territories of the Bahmanis or their successors. In fact, the rajas of Vijayanagra, as is well known, built their own mosques, evidently to accommodate the sizeable number of Muslims employed in their armed forces.
By contrast, monumental royal temple complexes of the early medieval period were considered politically active, in as much as the state-deities they housed were understood as expressing the shared sovereignty of king and deity over a particular dynastic realm. Therefore, when Indo-Muslim commanders or rulers looted the consecrated images of defeated opponents and carried them off to their own capitals as war trophies, they were in a sense conforming to customary rules of Indian politics. Similarly, when they destroyed a royal temple or converted it into a mosque, the ruling authorities were building on a political logic that, they knew, placed supreme political significance on such temples. That same significance, in turn, rendered temples just as deserving of peace-time protection as it rendered them vulnerable in times of conflict.
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Richard M. Eaton (Temple Desecration and Muslim States in Medieval India)