Secularism in the Islamic world has usually been forced from the top by governments. Major causes include WoT, Arab Spring etc. Biggest gains in places like Iran, retreats in places like Syria and Turkey. In the West, Secularism is on the retreat, even if due to culture wars (even Dawkins is now a "cultural Christian").
The issue with Pakistan is different. Unlike Christianity, Islam doesn't have a clergy/molvi class. We landed with one due historical reasons, post-colonisation. Since Pakistan is a secular state pretending to be an Islamic state, it still needs the molvi class as a buffer between it and a majority religious population. Iqbals's, "Mullah ko hai Hind main sajde ki azaadi, nadan samajta hai Islam azaad hai", is a criticism of this class. People can sense the problem but aren't educated enough to diagnose it, so the contradiction bursts out in form of mob violence. If you don't want molvi thuggery, either become an actual Islamic state (with separate legal system for minorities) and abolish the molvi class, or go full communist and destroy your people's identity like the Russians did in central Asia.
