India has been living with this polarization for the last 1000 years. Muslims were instructed by law to live separately from Hindus in the Indian islamic empires. I use the world islamic empire because this happened before the mughal rule.
The origin of "two nation theory" always existed, the British get wrong credit for this.
After such a long history and experience, it will take a LOT to "trigger" the Hindus into genocide. Even during the worst phase of islamic rule where hindus were second class citizens, slaves and hindu women and children were sold in bazaars, the Hindus formed the just and fair Vijaynagar Empire and the Maratha empire and gave equal right to muslims.
The problem is Muslims judge Hindus by THEIR OWN STANDARS and think Hindus will act like Muslims.
And "secular" Hindus who have drawn up and concluded a False Equivalence between Hindus and Muslims (same same) think along similar lines (only less brutal)
Which is why Muslims and "secular" Hindus Love to talk about "Hindu Taliban". An oxymoron if there ever was one.