The instigated riots were handled poorly by Operation Searchlight. However, rebellion of the masses can only mean that Bengalis were never sincere to the Pakistan movement. The Bengali elite saw it as means to a self serving end.
Bangladesh has absolutely nothing to do with Bengali sultanate nor Bengali identity less for Lahore Resolution '40.
It's not as black and white. Bengalis were among those leading the Pakistan movement prior to partition. The partition of India would not have taken place if Bengalis with such large population did not push for it.
Since 1947, you also have to take other factors into consideration to understand why people took up arms. I am just briefly going to list some -
1. The language issue in 1952.
2. The perceived lack of development in the East compared to the export earnings it was generating and compared to the development happening in the West.
3. 1965 war - leaving East Pakistan defenceless. Soldiers of East Bengal Regiment were fighting to save Lahore, and yet EP was left defenceless. This eventually led for one of the demands of the famous/infamous 6-points by Mujib, which called for establishment of Pakistan Naval HQ in EP.
4. The 1970 cyclone - the devastation it caused and the perceived lack of effort by the Central government in providing assistance, from the perspective of general populace.
5. Significant Hindu Minority in EP, some of who had been sympathetic to India and actively following RAWs directive. To note - at the time of partition Hindu Bengalis were generally well off and more educated and in position of authority, courtesy of them being more obedient to the Brits during colonial era. Post-partition they were in position of influence through media and academia. The military rulers in WP just made it easier for any subvertive agents to instigate the masses and influence thinking of the masses.
6. Communism - this was cold war. Communists were ideologically not aligned to Pakistan. The fact that Soviets intervened and kept US 13th fleet away shows that they were also very much active in the situation. However, it is often not much talked about.
7. Opportunists among Bengal Elites who saw separation as a means to enrich themselves.
8. Military Generals and their frequent meddling in governance.
9. Racism - hate it or deny it - it existed and still exists to date.
Now add a brain dead operation Search light to the mix and you get mass uprising.
The complex situation that developed in EP by 1970 needed finnese and cool headed diplomacy with compromise from both sides. Not brute force.
Mujib was willing to compromise on many grounds, but that needed reciprocation from the other side, which we didn't get courtesy of Bhutto and Yahya. The fact that post 1971 he went to Lahore to reconcile further proves that he didn't want a split up Pakistan. He didn't need to do any of that. He could have simply assimilated into Soviet Bloc.
And I personally believe that is what got him killed in 1975 by a combined RAW/KGB move. Contrary to current Sheikh Hasina's BAL govt. narrative that pro-Pakistan officers killed him. It does not make any sense whatsoever, because he was on track to mend relations with Pakistan and rest of the Islamic world, who at the time was in US camp. Only parties that could have been hurt by such move are Indians and the Soviets. Anyway, this is a discussion for another day.