We must remain sympathetic to the plight of any group that is facing such persecution. That they are Indian Muslims is irrelevant. Tens of millions of normal, law-abiding Indians will lose their legal status despite being born in the country and living there for generations. That is the only natural outcome of this process. If BJP wanted to grant citizenship to non-muslims they could do so already through administrative means by fast-tracking applications and highlighting back-logged cases in media. Instead, the BJP went further to codify exclusion of Muslims into the constitution so it cannot be challenged by Muslims and the politicians that support them.
The BJP knows it can't simply force the Muslim population to leave Islam at the barrel of a gun so instead they are trying to put them into a desperate, stateless position where they have no means of support and no vote. Over time these Muslims will choose to no longer identify as Muslims to avoid the detention camps and other indignities. Expect to see millions of Muslims, including many living in India for generations whose documents are rejected, change their name to remove their public identity even if they are still Muslim at heart. This is perfectly acceptable to the BJP which wants to destroy the public visibility and acceptance of Islam in India.