The way I am going to deal with it is like my old DM dealt with it in a previous 3.5 campaign where we made up a mini-game of kingdom building within the campaign (and why i chose to run KM)
basically the leadership feat allowed them to take control of an NPC which they had been grooming, and also took on responsibility for the welfare and health of said NPC. Without leadership any NPC's they wanted to be part of their kingdom were controlled by the DM and usually whined about food/jobs/freedom from oppression whilst not always following orders. The DM did ensure that the NPC was suitable for cohortness, i.e. the PC had been being friendly or done some actions over a period of time (generally over an entire level) that would mean that the NPC would follow the PC. Also if the PC neglected the new cohort then the cohort might decide that following the PC was not such a great idea and leave, causing all the penalties as if the NPC had died.