The NCAA isn't some organization put on top of the universities by some outside power. It is an organization of their own creation. The fact that it sucks is at least in small part Texas's fault. Mizzou is part of the organization so if they want to bitch about their penalties they can also look in the mirror. The organization sucks in part because its membership doesn't want to harm itself with penalties. Mizzou's ban affects the rest of the SEC and the SEC's bowl partners. I am sure schools in the other conferences are just as squeamish about this, which is why we see the standards for punishment rise and fall like the tides. With Penn State, Baylor and UNC issues the pendulum has swung back towards harsher punishment and Baylor looks to be the only one of the three in line for the potentially harsher punishment. (Pretty convenient, no?!)
The other issue that plagues the NCAA is the lack of subpoena power. Players are generally the only ones under scrutiny because the NCAA can dole out punishment knowing that few NCAA athletes have the means to lawyer up. When they do, penalties magically disappear. The Universities will never give up the power to govern themselves to some government agency that could compel testimony and evidence, so the NCAA sucks at enforcement largely by design.