East Pakistan and West Pakistan were devoutly Muslim but it didn't stop a war of independence by Bangladeshi nationalists breaking out.
By your logic Bangladesh should never have got its independence.
Actually ....
West Pakistan always considered themselves superior. There was a national election and the party from East Pakistan won 90% of the seats. The prime West Pakistan candidate had spent a lot of money in campaigning etc. and was psed. He told the East Pakistan party leader you can be the President of East Pakistan while I will be the President of West Pakistan. The leader replied saying WTF? The army did not want to be ruled by East Pakistan and imposed martial law and did a coup de tat. And, then the genocide took place over the years.
In Pakistan, even today, they lament what the leader did by not playing fair and blame him for the breakup.