The fact that those industries aren't conducive to a family lifestyle dissuades most LDS MBAs from pursuing them, and in turn, hurts the avg starting salary figures that are a big part of MBA rankings.

BYU grads by and large get the same or very close to the same starting salaries as their Stanford counterparts in the Bay Area in similar jobs. Marketing, corporate finance, HR, and supply chain jobs in the bay area (and most likely elsewhere) pay roughly the same no matter where you went to school (assuming in the top 30). The catch is that many of these companies will only recruit certain schools, but most recruit BYU.

Salaries in the bay area vs. the intermountain west are ~ 20-30% higher for the same job depending on the industry (the cost of living differential is even higher than the salary differential however), so with the fact that most Stanford grads stay in the Bay Area, and a much higher percentage of them will go into consulting, i-banking, or private equity, it's not surprising the avg starting salary is that much different.