Aga Khan was the leader of the Ismaili sect from Persia, which originated in the cult of the Assassins. It is closely related to Freemasonry. The Agha Khan was very close the to British rulers, and was the first President of the Muslim League. The Muslim League was used by the British to create Pakistan.
Incomplete research, what u are saying about the Aga khanis belonging to a creed of assasins from antiquity is false. They are known to be the Qizalbash by some.
Jinnah was originally an Ismaili, and he converted to Shi'ism only later. As such, his closeness to the Agha Khan would be natural. Jinnah was also very close to the Qadianis - in fact, it was the leader of the Qadiani community in London who was instrumental in Jinnah going back to India to lead the Pakistan movement.