First of all Iqbal passed away 11 years before the birth of Pakistan and 4 years before even the resolution through which Muslim League started demanding for a separate state for the Muslims of India.
Secondly, Sir Muslim League was a Bengali-UP creation. It all started in 1906 in the backdrop of division of Bengal. Bengalis along with Muslims from UP and Bihar were the driving force behind Muslim League. Name me two Punjabi, Pathan, Sindhi or Baloch politicians of the stature of Liaqat Ali Khan, Suharwardhy or Fazul ul haq.
If you try to study the dynamics of united Bengal before partition, you'll understand that of all the ethnic groups that joined to create Pakistan, Bengalis were the one who benefited most from it. See Punjabi Muslims were already pretty dominant in their province, same with the Pathans and Sindhis, the Baloch were also away from the yolk of Hindu domination. Bengali Muslims on the other hand were subject to oppression at the hand of the west Bengali elite. And the communal tensions were way higher there even before partition, take 1946 riots for example.
So saying that the Bengali Muslims wanted to stay with India is a blatant lie. They wanted Pakistan, they worked for it and yes we both messed up something beautiful resulting in creation of Bangladesh.