India had a huge population and was quite advanced in a number of fields - mathematics as has been mentioned, manufacturing (ie, wootz steel...) Militarily, however, it was not terribly successful. This wasn't a question of Hindu vs Muslim, it applied to any army based in the subcontinent. As far as I can think, no Indian-based military since the Cholas in the 11th century managed to conquer outside the subcontinent.
The main reason, according to sources at the time, is that most of the subcontinent was a terrible place to raise horses. The difficulty that Indian states had in acquiring horses, and the exorbitant prices they were willing to pay, is quite well-established.
That being said, it sounds like India should be able to resist conquest and assimilation. However, all states in CK ought to be able to better resist conquest and assimilation - particularly in an "old" civilization where the elite language, the vernacular, and the religion are closely interconnected, like India.
'Hinduism" as an actual "religion" didn't come into being until the 1950's, post-WWII.
Many modern Hindus overstate the degree to which Hinduism is and always has been a unified religion like the Abrahamic monotheisms, but you're going overboard here. Mass movements to create a unified doctrine of Hinduism date at least to the late 19th century. Medieval intellectuals recognized the idea of Hinduism, even if they didn't call it that. The most popular deities changed from time to time and place to place, but Sanskrit as a holy language, the narratives of the Ramayana and the Mahabharata, the Vedas, and a number of related concepts have all spanned the country from north to south for a couple of thousand years, at least.