This cooperative arrangement was selected for other reasons, not kinship. Another kind of false altruism. What was good for one was generally good for the other if they all had to reproduce through the same cells. If instead, the initial mitochondria could reproduce horizontally and move from one host to another, it might be advantageous to use up the host cell's food, burst out of the host and go find another to infect. Pathogens like viruses do this.
Organisms follow all three of the precepts of French revolution.
So the individuals are not a fixed step on the hierarchy of life. The individual is not a given as the unit of selection. In some case it was a group that came to be so unified by kin selection or by mutual benefit that it became a solidified unit of selection. Still, such transitions, though very important in the history of life, are exceptional and rare.