Considering the known fact the Pakistani government sponsored and backed the Taliban since it came to power in 1995, a direct connection between ISI and al-Qaeda would not surprise me. I doubt AQ is a subsidiary of ISI, but AQ has certainly penetrated the ISI.
At the beginning: The Al Qaeda was founded in August 1988, the same month that President Zia ul-Haq was killed in a plane crash in Pakistan. General Zia was expected to be a sponsor of Al Qaeda and his death was a blow to the nascent organization. It was hoped that the head of ISI would replace Zia, but that did not happen. In 1990 Osama had moved to Saudi Arabia, but his organization contined to operate in Afghanistan. After Obama moved to the Sudan he met on various occasions with former Pakistan military who were former ISI and committed Islamists. Meanwhile, Osama was helping to finance an Islamist training center at Murdike near Lahore, Pakistan, and it became important to both Al Qaeda and the ISI. In 1996, when Bin Laden left the Sudan he flew first to Pakistan before he continued to Afghanistan. It was thought that while in Pakistan he met with ISI principles in order to gain approval for his use of Peshawar as a safe-haven, and to gain an appreciation of the ISI involvement with the growing Taleban presence in Afghanistan. In sum, there is enough history of OBL-ISI involvement to speculate that the ISI was responsible for finding him a home in Abottabad, and protecting him thereafter.