A limited budget with which to hire his coaching staff.
KS couldn't get Jay Hill back when Kalani got the job or really, any time prior to Big 12 money becoming a reality. This has been publicly acknowledged since Hill's hiring. BYU had not yet given up on it's severely outdated model of trying to win on the cheap with a relative shoe string coaching budget.
Give Kalani a fair shot, and he's proven he can attract real coaching and staffing talent to Provo. Not every hire has been or will be perfect, but with a relatively reasonable playing field, he's acquitted himself very well.
Now the discipline thing--I agree wholeheartedly that he's had to learn some very difficult lessons and may have nearly lost his job during the painful process of ascending the learning curve. With the right people on the bus, things seem to have improved dramatically.