In this part of the world the Muslims are the traditionally down trodden section. Those who converted from Hinduism were the Lowest Castes of Hindus, and traditionally deprived of all civilised rights. Their erstwhile Masters could never accept this escape of their Slaves.
If you keep people bottled up, always under a microscope, and with no access to prosperity or modern education, then it is pointless to criticise their supersticious and ignorant behaviour.
Upper Hindus have never accepted modern Western ideas of equity and equal respect, whether to their own Slaves (called Lower Castes) or to their ex - Slaves (suspected to have converted to Islam and Christianity).
Partition was probably an Upper Hindu act of attempted Good Riddance, in order to achieve complete control, but it mis fired because the over whelming majority of Muslims stayed back in India.
I think the Upper Hindus will never willingly give up their dreams of supreme control, but they might be made irrelevant by the forces of Westernisation, Modern communications technology, and Western education.
However all that might take about a century more.
So the troubles of this region are likely to continue for a long time.