That was ideological requirement of the nations, How to justify the ideology of Pakistan without having anti-India ideology, for India, it was a good thing to blame for all fallacies of Indian part on Pakistan, Hindu nationalist were first to propagate two nations theory even though Deoband opposed it. Partition violence and subsequent loss is still in the living memory, it will take some more time before its eventual death.
I doubt maharaja’s secular credential as well, A country like India with secular constitution struggles to maintain secularism, how would a kingdom can do so? Akbar had Sulh-i-kul as state policy, Maharaja never had such thing, majority of population were Muslims,though Maharaja had many Muslim soldier as well as Muslim generals whose sensibilities were generally taken care of. Masjid was strategically located against the Lahore fort as well, sometimes during war it was even destroyed by shell fire from the fort.