in those times religion was a scant sixth in order of reasons and rationalisations for conquest and empire, then as now it was a technological advantage, guns, and the rajputs didn't have them, mobility, the rajputs were agrarian, the mughals were mostly pastoralists and always on the move.
but just so that you know, I have traveled through north west punjub, to muree, and lundi khotal, and there are ruins of stupas and things much much older that litter the landscapes, so to pick one particular starting point is disingenious, or worse.