A few points:
(1) There used to be a perception that academic excellence required reigning in football. I am not sure this is the case any more. In the new corporate atmosphere, I think they think of the latter as funding the former and helping create brand awareness.
(2) I do think it is still more difficult for ND to bend its rules and standards as compared to a giant state school. When there are 15,000 per class and the school is a giant bureaucracy and you never see the majority of kids in your graduating class, its not a jarring to give kids special treatment. In a small tight-knit atmosphere like ND, kids have to fit into the community more and live by its standards. Russell Wilson, yes, Jameis Winston, No.
(3) I think the big issue moving forward for ND decision-makers (at least on the religious and academic side of the equation, ie., the Holy Cross Fathers and the faculty) will be feeling dirty about spending so much on football in light of the school's secularized Catholic social mission. Just as the school de-emphasized football to take the next step in academic prestige, the school also re-thought its Catholic identity for the sake of academic prestige. While many Catholic schools in that transitional era pretty much shelved Catholicism completely, ND took the more moderate root of downplaying the devotional and doctrinal aspects of Catholicism, and playing up the social justice aspects that are generically cherished by academia at large. The school's Catholic mission becomes a kind of romantic, poetic commitment to pursuing certain policy goals that were already acceptable to academia (and, consequently, to corporate America). The areas of social justice that academia does accepted, but Catholicism embraces, are constantly downplayed or called into question. Long story short, in that atmosphere, if we claim that we are all about putting the world's resources at the disposal or the poor, weak, and vulnerable, should we really be spending $300M on an upgrade to already luxurious athletic facilities? The optics are just bad.